--- Log opened Sun Feb 05 00:00:56 2012
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00:26 < kanzure> "Received 16 December 1968. Available online 17 July 2002"
00:26 < kanzure> riiight...
01:35 < kanzure> http://tatoluis.ta.funpic.org/password18Septiembre.htm
01:36 < kanzure> http://groups.google.com/group/sci.med/browse_thread/thread/0638bc14a2ed74a7
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01:50 < kanzure> http://okulweb.meb.gov.tr/06/20/306107/downloads/library%20%C5%9Fifreleri.txt
01:52 < kanzure> some more http://literature-free.blogspot.com/
02:02 < kanzure> http://64.27.4.128/forum/index.php
02:05 < kanzure> http://hi.baidu.com/ezproxyvpnmd/blog/item/0f82d20c1e8c2e276159f331.html
02:05 < kanzure> pft they are just bruteforcing them
02:05 < kanzure> i'm so disappointed
02:05 < JayDugger> What, free doesn't impress you?
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02:12 < kanzure> http://www.databisnisekonomi.com/html/account/cn/2/
02:15 < kanzure> some relatively recent ones:
02:15 < kanzure> http://webcache.googleusercontent.com/search?q=cache:http://0618.us/post/3243/&num=100&hl=en&biw=1366&bih=626&strip=1
02:16 < kanzure> raw addresses with no passwords: http://soulofrain.wordpress.com/2011/10/05/ezproxy-list-no-password/
02:18 < kanzure> haha their tutorials are sad :/ http://blog.csdn.net/ananias/article/details/674089
02:22 < kanzure> ah here's a pretty active forum.. http://www.i-nobel.com/bbs/index.php
02:23 < kanzure> "Subject: 98,752 Posts: 515,068"
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02:59 < kanzure> i-nobel is pretty impressive
03:05 < kanzure> "[EBooks] Springer-Progress in colloid and of Polymer Science - Series uploaded (about 80 books)"
03:06 < kanzure> here's their polymer science subsection o.o http://www.i-nobel.com/bbs/thread.php?fid-905.html
03:06 < kanzure> "China Chemical Industry Group proposed an annual output of 10,000 tons of aramid production line "
03:08 < kanzure> drug design http://www.i-nobel.com/bbs/thread.php?fid-910.html
03:08 < kanzure> "Modified Nucleosides: in Biochemistry, Biotechnology and Medicine "
03:08 < kanzure> well that's oddly relevant..
03:12 < JayDugger> Anyone else here practicing intermittent fasting?
03:19 < kanzure> http://bbs.ok6ok.com/ seems to be the same thing
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03:57 < kanzure> lots of recent logins here: http://bbs.hx95.com/simple/index.php?t101852.html
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04:57 < kanzure> hi delinquentme
04:58 < delinquentme> howdy kanzure
05:21 < delinquentme> kanzure, how does a blastocyte differ from the magic of a blastocyst
05:44 < kanzure> delinquentme: pm
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06:26 < jrayhawk> JayDugger: I've looked into it slightly and played with it a little; intermittant carb fasting (maybe two weeks every three months or so) sends the body into ketosis, and periodic protein fasting (maybe 24 hours once a month) sends the body into autophagy, which both have some benefits.
06:28 < jrayhawk> Compressed eating windows are convenient if you're fat-adapted enough to comfortably implement them, but I'm not convinced there are any particular health benefits.
06:30 < jrayhawk> Compressed eating windows can lead to caloric restriction, which is theoretically good for longevity, but I think decreasing your quality of life to extend your quantity of life is a bit questionable.
06:36 < Mariu> depends on what someone finds important, some people might not trade their own life for quality and vice-versa
06:37 < Mariu> sorry for the poor wording
06:39 < Mariu> *depends which things are important for someone - maybe fixes it a little
06:41 < uniqanomaly_> foucist: http://ezproxy.free-webmaster-resources.org/
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06:57 < JayDugger> Thanks, jrayhawk. I've not had any trouble with I.F.. Really, I don't see how skipping two meals a day decreases one's quality of life.
06:59 < JayDugger> A few of the particular symptoms I noticed when I began recently returned, and I wondered if anyone here had encountered them. I suspect they involve a change in the amount, kind, or source of the protein I eat.
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06:59 < jrayhawk> Do tell.
07:00 < JayDugger> On which point?
07:01 < jrayhawk> particular symptoms
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07:03 < JayDugger> Halitosis and chills.
07:03 < JayDugger> The protein sources went from plant and algae and fish to just fish and animal over the last week.
07:03 < jrayhawk> Your "halitosis" is probably ketone bodies (acetone!)
07:05 < JayDugger> The chills only returned in the last twenty-four hours. In general, I've felt more comfortable than normal in temperatures about 45° F or so.
07:05 < JayDugger> This might well not matter. I always prefer cold weather.
07:06 < jrayhawk> Fun fact about ketosis: you can tilt breathalyzers by about .02 BAC with it.
07:08 < JayDugger> Heh. How fortunate I practiced reciting the alphabet in reverse.
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07:09 < JayDugger> Carbohydrate fasting means how low an intake per day?
07:09 < JayDugger> Say, in grams per day?
07:10 < jrayhawk> Depends on how it's implemented. If you're sedentary, probably 50-100.
07:10 < jrayhawk> Err, the limit is probably somewhere between 50 and 100
07:10 < delinquentme> education sucks because they're effectively asking you to select something you want to do for the next 4 years of your life
07:11 < delinquentme> 1) thats a LONG ass time
07:11 < jrayhawk> If you make a habit of depleting liver glycogen through exercise, it can be a lot.
07:11 < delinquentme> 2) even with what I know of current tech... I cannot look at something and say " YEH Im gonna do that day in and day out for the next 4 years "
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07:12 < jrayhawk> Anyway, after a few days of low-carbing, you can get a lot of starvation symptoms that usually go away by the two-week mark.
07:12 < jrayhawk> Brain fog, chills, etc.
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07:15 < jrayhawk> Ketosis is fascinatingly transformational; huge swaths of your expressed genetics change and basically every system in your body starts working more consistently.
07:16 < JayDugger> I had chills the first month or so of I.F., IIRC, but no brain fog. They never felt severe, only as if I'd a stomach full of ice water.
07:17 < JayDugger> I'd reduced carbohydrate intake to somewhere under a hundred grams per day a long time, years in fact, before starting I.F..
07:17 < jrayhawk> And only got horrible breath recently?
07:18 < jrayhawk> Weird.
07:18 < JayDugger> No, now that I think, that happened the first, oh, three weeks of I.F., then just again today.
07:19 < jrayhawk> You might play with probiotics; it's pretty easy to starve out strains in the gut and get weird effects as a result.
07:20 < jrayhawk> Gut biota have a very very deep and complex relationship with the rest of the body.
07:20 < JayDugger> That's a thought.
07:21 < jrayhawk> So, like, kimchi, sauerkraut, yogurt from grass-fed cows, also potentially various supplements
07:22 < JayDugger> Yuck, yuck, lactose-intolerant, and pills suit me fine.
07:23 < JayDugger> Why would grass-fed yogurt have a probiotic effect?
07:23 < JayDugger> I see that pastures provide a way to "inoculate" the dairy animal, but does it actually pass into the milk and on through the yogurt?
07:25 < jrayhawk> Even the less horrifying forms of grain-feeding have all sorts of negative nutritional effects on milk and meat.
07:26 < JayDugger> So I've read. I dislike most dairy products, so it never really bothered me much,
07:26 < jrayhawk> You can probably drink small quantities of unprocessed milk, which contains lactase, if ever you manage to find a source.
07:26 < jrayhawk> In many states it's illegal to retail, though.
07:26 < jrayhawk> Milk processors are rent-seeking dicks.
07:26 < JayDugger> No fucking way.
07:27 < JayDugger> I find raw milk disgusting. (My maternal grandfather had a dairy farm.)
07:27 < jrayhawk> Ah, but were they grain fed or grass fed?
07:27 < JayDugger> It was the appearance that turned my stomach.
07:28 < jrayhawk> you're... afraid of colloids?
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07:29 < JayDugger> Nope, just raw milk. I'd rather eat mud.
07:30 < JayDugger> Mud has the additional advantage of not needing lactase.
07:30 < jrayhawk> So, does coconut milk horrify you, too?
07:30 < JayDugger> No, that's fine.
07:30 < jrayhawk> but... they're visually the same thing
07:30 < jrayhawk> droplets of saturated fat suspended in water
07:31 < JayDugger> In general, I'd happily eat out of a dumpster. (Did that to win bets.) I just won't touch raw milk.
07:31 < JayDugger> And no, coconut milk doesn't remind me of raw milk.
07:31 < jrayhawk> I'm not about to argue that milk is a good idea generally, I just find this "appearence" thing very odd
07:32 < jrayhawk> like being afraid of the color blue or something
07:32 < jrayhawk> it's just such an abstract concept to me
07:32 < JayDugger> One of very few foods I won't eat, and yeah...not exactly rational.
07:32 < JayDugger> My wife won't eat microalgae. She can't abide the taste, but I like it just fine.
07:33 < JayDugger> It tastes like fish food, Tetra flakes, in particular.
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07:35 < jrayhawk> I used to have a childhood-derived horror of fish, but then I discovered that wild-caught fish are delicious.
07:36 < jrayhawk> Similar thing with nuts, now that I think about it.
07:36 < jrayhawk> I'm glad food quality is making a comeback.
07:38 < delinquentme> JayDugger, you've eaten tetra flakes?
07:39 < JayDugger> Yes, I've eaten Tetra flakes.
07:39 < JayDugger> They taste just like they smell.
07:40 < JayDugger> I will try almost anything. Yes, that includes dog.
07:40 < JayDugger> And yes, I've eaten dog. It tasted like soy sauce and rice.
07:40 < jrayhawk> perhaps you were tricked into eating soy sauce and rice
07:41 < JayDugger> Not so much tricked, as the vendor spoke very little English, and I speak no Chinese.
07:42 < JayDugger> He pantomimed a dog pretty convincingly, though.
07:42 < jrayhawk> "you! american dog! buy my soy sauce and rice!"
07:46 < jrayhawk> I guess I should say slow-cooked wild-caught fish are delicious
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08:03 < jrayhawk> i don't think dog is properly horrifying; what about fois gras or ortolan or this http://books.google.com/books?id=70njN4h46zEC&pg=PA147
08:09 < klafka1> what are tetra flakes?
08:10 < jrayhawk> pelletized dehydrated algae
08:10 < jrayhawk> plus other miscellaneous ingredients
08:11 < jrayhawk> oh no wait, tetra is the mineral one, right
08:11 < jrayhawk> durrr
08:12 < utopiah_> Will teaching children basic programming skills have a political impact? https://blogs.fsfe.org/samtuke/?p=255
08:12 < jrayhawk> http://www.drsfostersmith.com/1/1/11319-tetramin-tropical-flakes.html
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09:31 < JayDugger> I think, increasingly, programming counts as a new literacy.
09:32 < JayDugger> I wonder by analogy, literacy:programming::post-literate society:?
09:32 < JayDugger> Poorly chosen syntax on my part....
09:53 < delinquentme> JayDugger, interesting bits
09:53 < delinquentme> do you still look at dogs as pets?
09:54 < delinquentme> or with that event were they stepped down a notch
09:59 < kanzure> JayDugger: i think neil has argued enough to have won that literacy argument by ow
09:59 < kanzure> *by now
10:31 -!- Mokbortolan_ is now known as Mok_Away
10:31 < delinquentme> hey does anyone recall what that drug was which was administered to cancer patients
10:31 < delinquentme> basically it worked *TOO* well and ended up rupturing all the cancerous membranes and the patient ended up dying of something related to that fluid release
10:32 < delinquentme> someone in the anti-aging crowd talked about it
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10:40 < falmot_> http://ansistego.sf.net/shrooms-8.txt
10:41 < falmot_> i drove off some aliens by accident :|
10:41 < falmot_> the devil made me do it :|
10:41 < falmot_> but i'm who to blame if the singularity is now cancelled
10:41 < jrayhawk> Isn't it always the way. Going about your day, minding your own business, then boom, you've destroyed the singularity.
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10:59 < Mariu> later everyone
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11:28 < roksprok> does anyone have a suggestion for what microcontroller to use for an electrode array?
11:29 < roksprok> would it be better to use something like an arduino or beagleboard or just avr chips
11:30 < delinquentme> roksprok, how advanced are you?
11:30 < delinquentme> I'd also check out #robotics and #seattlerobotics
11:30 < delinquentme> AVRs are awesome if you're hardcore
11:30 < delinquentme> im a bit of a newb
11:30 < delinquentme> so I went w the arduino
11:31 < roksprok> i've done a couple arduino projects but thats about as far as i have gone
11:32 < roksprok> have you found that its limiting you in anyway?
11:33 < roksprok> i'm trying to decide wether to just jump in with arduino or bite the bullet and learn avr programming
11:33 < roksprok> *whether
11:34 < roksprok> i'd like to be able to make something like this http://www.zachhoeken.com/mouthbrain
11:34 < roksprok> it sits on the tongue
11:35 < roksprok> so its not exactly what i have in mind
11:36 < roksprok> but in general its similar in that its bidirectional and has 256 total electrodes
11:39 < roksprok> I've found a bit on different ways of fabricating electrodes
11:39 < roksprok> but so far the only 'complete system' is modulareeg which seems to not be supported much anymore
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11:41 < delinquentme> roksprok, well if you're wanting to build big ass mcnasty robotics
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11:41 < delinquentme> the _ONLY_ issue i had with an arduino
11:41 < delinquentme> wait
11:41 < delinquentme> 2 things
11:42 < delinquentme> 1 installing the IDE on ubunter
11:42 < delinquentme> ( was a pain ... but i think its been improved )
11:42 < delinquentme> 2 the clock speed working within the arduino env... but there was a hack to get it to cycle faster by running it off of the AVR clock or something
11:44 < roksprok> delinquentme: 2 is kind of what i'm worried about. if i'm going to have to use workarounds and hacks anyway I may as well invest the extra effort in learning the avr language
11:45 < delinquentme> roksprok, if you're just tinkering arduinos are awesome
11:45 < delinquentme> BUT
11:45 < delinquentme> i also just realized i havnt checked out the support thats available in an AVR channel
11:45 < delinquentme> i think anyone in #robotics will tell you to go w AVRs
11:46 < delinquentme> but they also teach intros to robotics w the arduino
11:46 < roksprok> delinquentme: there is a forum called avrfreaks that seems like it would be supportive
11:46 < roksprok> so i think i'm going to go that direction
11:47 < delinquentme> roksprok, forums are good
11:47 < delinquentme> but IRC SOOOO much faster
11:48 < roksprok> delinquentme: and probably better for beginners, as I wouldn't be clogging up a forum with newb questions
11:49 < delinquentme> roksprok, ummm
11:49 < delinquentme> while its a generous thought
11:49 < delinquentme> just tell people you're new ... and just dig into paying attention to what they say
11:50 < delinquentme> people are surprisingly helpful when you can ask specific questions and you're patient :D
11:50 < delinquentme> seriously i still dont comprehend the awesomness that is IRC but people want to help others
11:50 < roksprok> delinquentme: cool that is reassuring
11:50 < roksprok> thanks for your help
11:51 < roksprok> i just started on irc and am already amazed at how much free knowledge is out there
11:54 < delinquentme> roksprok, i just posted to FB about how it blows my mind
11:54 < delinquentme> :D
11:55 < delinquentme> not only that but people are willing to troubleshoot YOUR problems
11:55 < delinquentme> and its even crazier than that ... bc they dont know your from adam!
11:59 < roksprok> yeah its really amazing
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12:32 < jrayhawk> okay what about eating a mokbortolan bunting
12:45 < delinquentme> O_o
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16:30 < kanzure> neat, an opml rss file
16:30 < kanzure> http://feeds.sciencedirect.com/opml.xml
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16:53 < kanzure> license file
16:53 < kanzure> http://web.archive.org/web/20000302122142/http://www.web-editions.com/web_editions_license.pdf
16:56 < kanzure> or here http://web.archive.org/web/20050218014837/http://www.web-editions.com/license.html
16:57 -!- Troletariat is now known as Omega
16:58 < n_bentha> o/ I searched a sequence of a plasmid on blast, and there's a short "synthetic" sequence outside of the MCS that's also a restriction site for BSTEII enzyme. BSTEII cuts in this "synthetic" sequence as well as in the MCS. If I'm inserting a fragment of dna that's ~1000bp that was cut with the BSTEII enzyme, would I expect 2 types of plasmids. One with 2 inserts, and another with 1 inserts of my sequence?
17:01 < yashgaroth> you would get several different ligated combinations
17:02 < kanzure> hm the margins are 35%
17:03 < yashgaroth> you'd be inserting the fragment in place of the region between the two sites on the plasmid that got cut
17:04 < n_bentha> oh...i see...
17:04 < n_bentha> yes you're right. i guess it's better to use 2 different enzymes for specificity?
17:05 < yashgaroth> is there another site in the MCS with compatible sticky ends with BstEII?
17:06 < yashgaroth> also it really depends on the plasmid and the fragment
17:07 < n_bentha> oh i don't think there is another compatible sites...
17:07 < yashgaroth> yeah probably not but it was worth a shot
17:09 < yashgaroth> well what's the plasmid?
17:10 < n_bentha> pcambia309
17:12 < yashgaroth> 0390?
17:15 < yashgaroth> it's very odd they'd have a second site for an enzyme that's already in the mcs
17:17 < n_bentha> it's a modified version, yashgaroth
17:18 < yashgaroth> you have a link to the sequence?
17:21 < n_bentha> to the pcambia sequence?
17:21 < yashgaroth> yuss
17:24 < yashgaroth> at least the one where you found two Bst sites
17:25 < n_bentha> http://www.ncbi.nlm.nih.gov/nucleotide/AF406991?
17:30 < n_bentha> see?
17:30 < yashgaroth> indeed
17:31 < yashgaroth> well you could try picking a different site in the mcs and chewing off the sticky ends, then doing blunt end ligation
17:31 < yashgaroth> but that has rather low efficiency
17:33 < yashgaroth> or design primers to overhang your fragment that have a better enzyme site on them
17:34 < yashgaroth> ^which would also allow you to not have to make sure the insert is in the proper orientation
17:35 < n_bentha> ah ok
17:37 < n_bentha> so would i need to make a cut w/ the enzyme, and then add the primer that would bind both the fragment and plasmid?
17:38 < yashgaroth> you need primers where the 3' end overlaps the end of your fragment, and the 5' end has the restriction enzyme site you want
17:38 < yashgaroth> after you pcr it up you can cut it with those sites' enzymes and have new sticky ends that match your plasmid
17:41 < kanzure> yashgaroth: hey i was thinking about doing an oligo library again,
17:41 < kanzure> and the best way to do it would be if i can have a library of <rs>oligo<rs>oligo<rs>oligo oligomers
17:42 < kanzure> this way, it's long enough to pcr and replenish the library supply
17:42 < kanzure> but down-stream dna ligation (of library items) is probably effected by how that restriction enzyme process would work
17:42 < kanzure> any ideas
17:43 < yashgaroth> if you want unlimited amounts of it, I'd recommend keeping it in a bacterial plasmid to grow up, rather than pcr
17:43 < kanzure> the context is the microfluidic device- so in this scenario there'd be a few thousand droplets, each with a single type of library item
17:43 < yashgaroth> ahh
17:43 < kanzure> one-cell-per-droplet or some-culture-per-droplet is doable
17:43 < kanzure> but access times (growth + harvesting + purification) would be horrible
17:44 < yashgaroth> so each oligomer has one type of oligo?
17:44 < kanzure> i mean one 'sequence'
17:44 < delinquentme> my panacea for religion, morality, congress and the senate: http://www.reddit.com/r/fuckingphilosophy/comments/oxemc/fucking_ethics_how_do_they_work/c3o9qfg  if anyone cares to pick my brain =]
17:44 < kanzure> like imagine a 6mer library of all 6mer permutations
17:44 < kanzure> you can't pcr a 6mer really
17:44 < yashgaroth> no you cannot
17:44 < kanzure> soo one way to make it longer is arbitrary/lame restriction sites
17:45 < yashgaroth> then you're limited to oligos that can be cut by enzymes
17:45 < kanzure> no.. you'd synthesize your oligos once to include the restriction sites
17:45 < kanzure> <rs>o<rs>o<rs>o<rs>o
17:45 < kanzure> erm probably with an ending <rs>
17:45 < n_bentha> what's the way that viruses make their -mers?
17:45 < n_bentha> don't they make 16-mers?
17:45 < yashgaroth> what, all viruses?
17:46 < n_bentha> some*
17:46 < yashgaroth> kanzure: but the oligos still have the sticky ends from whatever enzyme you use
17:47 < yashgaroth> which limits your ability to synthesize a sequence of your exact choosing
17:48 < kanzure> perhaps there's some other scheme :/
17:48 < n_bentha> oh i think it's t4 and t7 viruses
17:49 < yashgaroth> oh you mean when they replicate their genomes?
17:49 < n_bentha> yes, they form concatemers
17:51 < kanzure> yashgaroth: wuddabout extension pcr instead
17:51 < kanzure> that's a thing right, i'm not misremembering?
17:51 < kanzure> http://www.gardnerlab.org/protocols/oePCR.htm
17:51 < kanzure> "This type of PCR is used to make mutations, fuse two gene segments together, make insertions within a gene, or make deletions within a gene."
17:52 < n_bentha> yashgaroth: you said that i could use 'compatible enzymes', right? if i use ecori, it'll cut once in the plasmid and once in the gene i'm inserting. so can i use MfeI to make a compatible sticky end instead?
17:52 < yashgaroth> kanzure: you mean for generating oligos or for bentha's thing?
17:53 < yashgaroth> you're cutting your gene fragment with the enzyme, or is it in another plasmid that has flanking Eco sites?
17:54 < kanzure> yashgaroth: my thing :3
17:54 < n_bentha> gene fragment
17:54 < yashgaroth> no then you'll just have two subfragments of your gene, each with a Bst and Eco site
17:55 < n_bentha> i'm just making sure if i cut my plasmid with ecori and i cut my gene fragment with MFeI, that it'll bind
17:55 < yashgaroth> your fragment has an Mfe site somewhere in the middle?
17:55 < n_bentha> i don't think i'd use the bsteII REN...
17:56 < n_bentha> yes, yashgaroth. (i'm not concerned about the functionality of the gene)
17:57 < yashgaroth> you...might end up with the two halves of your gene in the site, in the wrong order, but if you don't care about a functioning gene then why are you inserting it?
17:58 < yashgaroth> kanzure: I'm not seeing how overlap pcr applies...you mean for ligating the single oligos together?
18:14 < kanzure> yashgaroth: growing oligo will be attached to a bead
18:36 < n_bentha> ok thanks guys, i've got 3 different combinations of enzymes i can use now :)
18:36 < n_bentha> with different lengths of the gene resulting
18:43 < yashgaroth> what gene are you using and why?
18:47 < n_bentha> secret
18:47 < yashgaroth> heh I can respect that
18:48 < n_bentha> don't want to get scooped!
18:55 < n_bentha> but if you look up the plasmid, you can find out kinda what i'm doing w/ it
18:55 -!- JayDugger [~duggerj@pool-173-74-78-36.dllstx.fios.verizon.net] has quit [Quit: Leaving.]
18:58 < n_bentha> http://www.springerlink.com/content/p162852283850l3x/#section=95251&page=1&locus=4
18:58 < n_bentha> virally induced gene silencing
18:58 < n_bentha> but i gtg, i'll let u know how the plasmid goes
18:59 < kanzure> come back and visit sometime
18:59 -!- n_bentha [~lolicon@75.111.160.104] has left ##hplusroadmap []
18:59 < kanzure> can someone get me a dns server other than 8.8.8.8 and 8.8.4.4?
19:00 -!- klafka [~textual@c-71-204-150-80.hsd1.ca.comcast.net] has quit [Quit: Computer has gone to sleep.]
19:01 < kanzure> ah nevermind
19:04 -!- klafka [~textual@c-71-204-150-80.hsd1.ca.comcast.net] has joined ##hplusroadmap
19:05 < kanzure> "Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides"
19:05 < kanzure> hmm
19:08 < yashgaroth> the problem is that you're using either short oligos that are hard to reliably assemble, or large oligos in which case you still have to generate long strands anyway
19:10 < yashgaroth> but then, I'm perfectly happy splicing just genomic and/or commercially available sequences
19:16 < kanzure> yashgaroth: http://www.springerlink.com/content/141730735j433414/
19:17 < kanzure> they suggest using dsDNA and not necessarily ssDNA
19:17 < kanzure> but it looks like their method relies on primer overhangs, i'm still looking
19:23 < kanzure> not fair.. they are synthesizing custom primers i think
19:24 < yashgaroth> it does look that way
19:24 -!- klafka [~textual@c-71-204-150-80.hsd1.ca.comcast.net] has quit [Quit: Computer has gone to sleep.]
19:27 < kanzure> if you're synthesizing 20bp primers you might as well just combine these fragments together to make whatever it is that you want
19:27 < yashgaroth> which is the current commercial method
19:28 < kanzure> so.. why do they think oligo synthesis /plus/ extension pcr /plus/ all these other steps are worthwhile?
19:30 < yashgaroth> looks like that paper's more for library generation than gene synthesis
19:31 < kanzure> library generation? i thought assembly :x
19:31 < kanzure> also, apparently there's such a thing as template-directed ligases
19:31 < yashgaroth> well, you have to assemble libraries
19:32 < kanzure> i should go read some sloning stuff. i thought slonomics corp solved a bunch of these issues
19:34 < kanzure> http://www.biotechniques.com/multimedia/archive/00003/BTN_A_000112953_O_3841a.pdf
19:37 < kanzure> "This permits the fully-automated synthesis of any 462 bp DNA fragment, from design to end product, within a time frame of 44 hours"
19:38 < kanzure> i don't like this world.
19:38 < yashgaroth> you mean biology in general or just gene synthesis
19:38 < kanzure> no i mean it's just disappointing that it's 2012 and here we have a method doing only 40.5 bp/hr
19:39 < kanzure> *10.5 bp/hr
19:39 < kanzure> phosphoramidite synthesis is ostensibly faster
19:40 < yashgaroth> oh it totally is
19:40 < yashgaroth> on both points
20:15 < Stee|> y'all use qiqqa, right?
20:18 < yashgaroth> programs similar to it
20:19 -!- roksprok [~Zac@74.83.205.124] has left ##hplusroadmap []
20:19 -!- roksprok [~Zac@74.83.205.124] has joined ##hplusroadmap
20:20 < yashgaroth> hmm android app and character recognition, looks pretty snazzy
20:24 < Stee|> auto-ocr
20:24 < Stee|> auto-sync
20:24 < Stee|> markup
20:30 < yashgaroth> soo who feels like getting me a copy of http://online.liebertpub.com/doi/abs/10.1089/hum.2011.102 ?
20:31 < Stee|> gimme a few
20:31 < yashgaroth> HGT used to have a policy of the current issue being free, but then they became dicks
20:46  * delinquentme eff just learned about 'chirality' and i begin to question whether any molecule is really chiral
20:46 < yashgaroth> erm how do you mean
20:47 -!- eudoxia [~eudoxia@r186-52-182-83.dialup.adsl.anteldata.net.uy] has quit [Quit: Leaving]
20:47 < Mok_Away> it's the gyres man
20:47 < Mok_Away> THE GYRES!
20:47 < delinquentme> yashgaroth, i've just played through my head a few examples of molecules and maybe i just didnt build them complex enough .. but none of them were chiral
20:48 < delinquentme> but its a tangent
20:49 < yashgaroth> all bioactive amino acids are chiral?
20:49 < delinquentme> yashgaroth, 3d molecule or it didnt happen
20:49 < delinquentme> like i trust you just say the word and I shall be healed
20:50 < yashgaroth> k http://en.wikipedia.org/wiki/File:L-alanine-3D-balls.png
20:50 < delinquentme> is that blasphemy ?
20:50 < delinquentme> yeah i think thats blasphemous.
20:50 < yashgaroth> that's not the term I would use
20:51 < delinquentme> nope i dont think thats chiral
20:51 < delinquentme> like heres a thought statement
20:51 < delinquentme> nm
20:51  * delinquentme ponders
20:52 < delinquentme> OHHHHH
20:52 < yashgaroth> on a scale of 0 to whooooa maaaan, how high are you right now
20:53 < delinquentme> "lacks internal plane of symmetry and thus has a non-super imposable mirror image"
20:53 < delinquentme> lolol
20:53 < delinquentme> i thought it meant that you cant take a mirror image of it
20:53 < yashgaroth> the mirror image would be the other isomer
20:53 < delinquentme> the mirror image being superimposable makes a difference
20:53 < delinquentme> yar
20:54 < delinquentme> whats the ship say in hitch hikers guide
20:54 < delinquentme> "normality restored" ?
20:58 < delinquentme> yashgaroth, srsly i was about 4 seconds from a nobel science prize in my mind
21:00 < yashgaroth> heh
21:07 < delinquentme> holy carp
21:07 < delinquentme> have I been using the word perogative all along?
21:07 < delinquentme> as in my perceptions are my "perogative"
21:08 < yashgaroth> ehh that's basically how it's pronounced anyway
21:09 < delinquentme> prerogative
21:09 < yashgaroth> yeah but no one ever says the first 'r'
21:17 < delinquentme> ok cool so im not nuts
21:18 < delinquentme> SOOOoo
21:18 < delinquentme> im shrinking a shrink
21:18 < delinquentme> purposefully picking on a poor old woman whos writing about sexual liberation for males via porn abstainance
21:18 < delinquentme> to convince her that its not so much porn shes worried about but instead her own death
21:19 < delinquentme> am I a horrible person?
21:19 < delinquentme> well porn >> being compared to prettier / younger girls // aging >> death
21:19 < delinquentme> porn > death was a prett big leap
21:19 < Mok_Away> even old girls need lovin' too
21:20 < yashgaroth> well, sex and death are the two drivers of psychology
21:22 < yashgaroth> so if she took one I guess you're stuck with the other
21:22 < delinquentme> Mok_Away, i havnt seen you talk here before :D howday
21:22 < delinquentme> yashgaroth, !
21:22 < delinquentme> yeahhhh  hahaha
21:22 < delinquentme> are there only two?
21:22 < delinquentme> or are those the primary 2
21:22 < yashgaroth> p. sure mok is mokbortolan btw
21:22 < delinquentme> of which all others stem?
21:22 < yashgaroth> no those are the only two
21:23 < delinquentme> jealousy >> sex
21:23 < delinquentme> check
21:23 < delinquentme> not bad i cant refute it yet
21:23 < delinquentme> yashgaroth, +10 points
21:23  * yashgaroth bows
21:28 < delinquentme> yashgaroth, http://scienceexchange.com/project_briefs/1311  << is this an easy project
21:28 < delinquentme> from what it sounds like there are 2 parts.. the database and the implementation of the search
21:28 < delinquentme> do you get that too?
21:29 < Stee|> wonder if I could get an rss feed of science exchange
21:30 < yashgaroth> I wish they'd have more than a 2 sentence description
21:31 < yashgaroth> all known human genes should already have their exons mapped out
21:31 < kanzure> delinquentme: Mok_Away is just mokbor
21:31 < Mok_Away> huhwhat?
21:31 < kanzure> ninja'd
21:32 < kanzure> by yashgaroth. crap.
21:32 < yashgaroth> :D
21:32 < Mok_Away> delinquentme: Howdy!
21:32 < delinquentme> Mok_Away, COOL ill keep an eye out
21:32 < kanzure> delinquentme: ok i'm still confused are you wanting to do work on scienceexchange as a person paying for work, or getting paid for work
21:32 < Mok_Away> Ok
21:33 < delinquentme> kanzure, so the description of that project seems simple as hell
21:33 < yashgaroth> side note, 'splice isoforms' is just begging to be re-termed spliceoforms
21:33 < delinquentme> and its totally bioinformatics specific work
21:33 < delinquentme> 1 id get paid 2 id have more work to referece
21:33 < delinquentme> check.
21:33 < kanzure> ok why don't you want to work for me
21:33 < kanzure> :|
21:34 < kanzure> haah maybe it's better you don't answer that
21:34 < Mok_Away> why, are you hiring?
21:34  * Mok_Away does Windows.
21:34 < kanzure> Mok_Away: sorta kinda,
21:34 < Mok_Away> I'm hiring for anybody with a GC/MS
21:34 < kanzure> there's two things that i am on the look out or
21:34 < kanzure> *for
21:35 < kanzure> one is someone that i can throw money at so that i don't feel so lonely pursuing my projects on my own
21:35 < Mok_Away> or even just a GC
21:35 < kanzure> second is that i sometimes end up with too much contracting work and it's nice to filter that out to friends..
21:35 < Mok_Away> what kind of contracting?
21:35 < delinquentme> kanzure,  what do you need coded?
21:35 < delinquentme> slash worked on
21:35 < kanzure> mobile (iphone, android, tablets) apps, web apps (python, ruby)
21:36 < kanzure> is the commercial stuff that comes my way.
21:36 < delinquentme> Mok_Away, what is a GC
21:36 < Mok_Away> Gas Chromatograph
21:36 < delinquentme> ahhh
21:36 < delinquentme> newp!
21:36 < Mok_Away> :(
21:36 < delinquentme> kanzure, python ill run with ... ruby as well
21:36 < delinquentme> id be willing to learn some java
21:36  * Mok_Away knows VBScript!
21:36 < delinquentme> ^^^^^
21:37 < Mok_Away> and now I have to learn pascal
21:37 < kanzure> so anyway, i think i could probably pay for someone to be full time at low pay
21:37 < kanzure> for "helping me out on various transhumaisty projects" thing
21:38 < kanzure> and even better if i can convince that person to live in a workshop somewhere >_<
21:38 < Mok_Away> If I didn't have a family to support I'd be on that like white on rice
21:42 < Stee|> kanzure, clearly you should fly eudoxia to the US to be an intern between finishing HS and starting uni :P
21:42 < kanzure> where is he, again?
21:42 < yashgaroth> wait is he actually in uruguay?
21:42 < kanzure> apparently
21:43 < kanzure> imho that was a dumb choice of his but w/e
21:43 < Stee|> dumb choice? O_o
21:43 < yashgaroth> ehh at least he's in a vaguely US timezone
21:43 < Stee|> I, uh
21:43 < Stee|> don't think that's a choice
21:43 < kanzure> Stee|: uruguay
21:43 < kanzure> of course it's a choice?
21:44 < kanzure> or are we talking "there are no such things as choices, man"
21:44 < Stee|> we are talking he hasn't lived anywhere else yet?
21:44 < kanzure> i'm not sure anymore
21:44 < Stee|> I mean
21:44 < Stee|> that's where he grew up
21:44 < Stee|> he didn't move there
21:44 < kanzure> i see
21:44 < kanzure> ok why is he still there?
21:45 < Stee|> finishing highschool
21:45 < yashgaroth> why are you still in texas
21:45 < kanzure> that's a lame reason
21:45 < kanzure> yashgaroth: i ask myself that every day
21:45 < kanzure> i have no reasons left, so i'm moving
21:45 < yashgaroth> good man
21:45 < Stee|> where to?
21:45 < kanzure> that's classified by the fbi
21:46 < Stee|> I don't even want to know how many watch lists you're on
21:46 < kanzure> wouldn't it be weird if it's none :/
21:46 < yashgaroth> I'm sure agent You has you at the top of his list
21:46 < kanzure> he has himself at the top of his list?
21:47 < kanzure> oh oh
21:47 < yashgaroth> in fact I'd be a little disappointed if he's not reading this right now
21:47 < kanzure> prepare to be disappointed :(
21:47 < yashgaroth> aww shucks
21:47 < kanzure> it's not like he sits around all day reading irc logs at midnight on sunday
21:48 < yashgaroth> it's the FBI dude, apparently that's all they can manage
21:49 < delinquentme> lady replied!
21:50 < delinquentme> she who is perfectly happy with her attractiveness ... spaced on answering the question at hand ... and instead goes on to justify her attractiveness
21:50 < delinquentme> crazy crazy shit our psychology
21:50 < Mok_Away> ..oh man
21:50 < Mok_Away> read the wiki page on cognitive bias
21:50 < Mok_Away> err, the list of cognitive biases
21:51 < delinquentme> ach
21:52 < delinquentme> feels like  http://nooutcasts.org/wp-content/uploads/2010/05/neo-wakes-up-within-the-matrix.jpg
21:53 < Mok_Away> like the day I learned thateveryone is an irrational asshole and discussion is largely purposeless
21:53 < Mok_Away> And also that "everyone" includes myself
21:54 -!- Mok_Away is now known as Mokstar
21:55 < delinquentme> Mokstar, there are as many realities as there are individuals?
21:55 < kanzure> hmm "DNA fragment sizing by single molecule detection in submicrometer-sized closed fluidic channels"
21:55 < delinquentme> seriously i feel like a bit of an asshole right now ... like I kinda mind-injected this lady
21:56 < kanzure> delinquentme: i was serious about my no MWI rule in here
21:56 < delinquentme> like i kind of feel bad
21:56 < Mokstar> MWI?
21:56 < kanzure> multiple-world interpretation stuff
21:56 < Mokstar> Messing With Imbeciles?
21:56 < delinquentme> OHHHHHH
21:56 < delinquentme> nah i can see why
21:56 < delinquentme> check no problems
21:56 < delinquentme> but really should I not do these things?
21:57 < Mokstar> naa, go for it
21:57 < kanzure> talk with people?
21:57 < kanzure> yes, you should stop talking with people
21:57 < delinquentme> like im worried about this ladies mental state
21:57 < kanzure> and get back to work.
21:57 < delinquentme> LOLOLO
21:57 < delinquentme> <3
21:57 < kanzure> delinquentme: there are many people with horrible mental states
21:57 < delinquentme> but I dont want to be the cause of it!
21:57 < kanzure> this is largely a failure of our knowledge of mental health
21:57 < delinquentme> like i feel  BAD so im in r/suicide watch doing pennance now
21:58 < kanzure> people who need suicide watch should not be getting it from some reddit user
21:58 < Mokstar> well, if you want to make amends you can offer your services to her in recompense
21:59 < Mokstar> "That ain't no cougar, that's a lioness!"
22:00 < delinquentme> LOLOL
22:00 < kanzure> didn't someone use dna as a waveguide for something
22:00 < kanzure> where did i see this :(
22:00 < delinquentme> kanzure, actually I think im a pretty good reddit suicide watch helper :D
22:00 < delinquentme> im on the front lives of saving lines BRO!
22:05 < kanzure> neat, "Simultaneous measurements of the flow velocities in a microchannel by wide/evanescent field illuminations with particle/single molecules"
22:06 < delinquentme> OOOO
22:06 < delinquentme> is this a chemically inert molecule?
22:06 < delinquentme> yashgaroth, can something be chemically inert to the point where it will react with *nothing*
22:06 < kanzure> well you can always just count beads going by
22:06 < delinquentme> or at least nothing biological?
22:07 < delinquentme> AH!
22:07 < kanzure> delinquentme: noble gases
22:09 < yashgaroth> some noble gases have been fluoridated
22:09 < Mokstar> insults don't work on the noble gases, they just don't react
22:10 < delinquentme> :D
22:17 < Stee|> so I got this sweet chair for my birthday
22:17 < Stee|> it is fucking fantastic
22:17 < Stee|> it's an exercise ball on a special holder
22:17 < Stee|> and you can take the exercise ball off
22:17 < Stee|> so now I can do ab work while thesis writing
22:18 < Mokstar> how does this work? http://www.cnn.com/2011/TECH/innovation/03/04/mobile.microscope.ozcan.malaria/index.html
22:19 < kanzure> Stee|: hey what happened to the "hire someone to punch you in the abs" plan
22:19 < kanzure> because of the "muscular damage" theory of muscle growth
22:19 < yashgaroth> I thought that was my plan
22:19 < kanzure> fuck
22:19 < kanzure> wait, i mean, no you were scooped
22:19 < yashgaroth> also you should probably combine it with tazing to get the contractile theory covered as well
22:20 < yashgaroth> in fact just resist arrest until you're schwarzenegger
22:22 < delinquentme> LOLOL
22:22 < delinquentme> but no really the punching method words
22:23 < Mokstar> did you try it?
22:23 < delinquentme> Mokstar, would you please post that to hacker news with the title something along the lines of " software 'innovators' gonna hate "
22:24 < delinquentme> Mokstar, i was actually part of a trial which i didnt really have consent on
22:24 < delinquentme> while this is conjecture
22:24 < delinquentme> throught highschool my friends would slug the shit out of my biceps
22:24 < Stee|> microtears :P
22:24 < delinquentme> and to this day i've got wild strong biceps
22:24 < delinquentme> and if you think about it
22:24 < delinquentme> what are you *DOING* while lifting
22:25 < delinquentme> you're not getting stronger
22:25 < delinquentme> you're tearing muscle fibers
22:25 < delinquentme> you get stronger while *HEALING*
22:25 < Stee|> in specific ways, yes
22:25 < yashgaroth> mok, isn't that article the same principle as shining a laser through a drop of pond water and seeing all the organisms?
22:25 < kanzure> i still think the damage/healing stuff is an insufficient molecular explanation :(
22:26 < kanzure> 1) get a fluoresence microscope
22:26 < delinquentme> kanzure, give me the mechanisms of which muscles contract
22:26 < kanzure> 2) spin up a muscle cell culture
22:26 < kanzure> 3) puncture it
22:26 < kanzure> 4) take mRNA readings periodically
22:26 < delinquentme> kanzure,
22:26 < kanzure> this shouldn't be hard.
22:26 < delinquentme> how about we get a place in SF
22:27 < delinquentme> and i just slug the shit out of your right arm ONLY
22:27 < kanzure> muscle contraction is myosin/actin
22:27 < delinquentme> for 2 months
22:27 < kanzure> lookup the myosin/actin/calcium rhetoric it's pretty thorough
22:27 < delinquentme> infact well get a house full of kids and see if we can reach a statistically valid sample size
22:28 < Stee|> kanzure, my buddy Andre is going to be joining us here and at my site soon
22:28 < Stee|> he's biomed, with focuses in fitness and neurobio I think
22:28 < yashgaroth> ooh can we make sure all the kids have muscular dystrophy? that's what all the research on this is under the guise of
22:28 < Stee|> working at a stem cell clinic over the summer
22:28 < delinquentme> Steel FUUUUUU
22:28 < Stee|> he knows all the most recent shit on muscle growth I think
22:28 < delinquentme> i want to be at a stem cell clinic
22:28 < Stee|> yeah
22:28 < Stee|> this is a stem cell injection clinic
22:28 < kanzure> someone needs to tell delinquentme about CIRM
22:28 < Stee|> down in miami beach
22:29 < delinquentme> kanzure, emailed em
22:29 < delinquentme> do you have hookups there
22:29 < delinquentme> tell them to let me program (FOR FREE)
22:29 < delinquentme> for them
22:29 < kanzure> not to my knowledge
22:30 < kanzure> how about bgi? you might have to go to china though
22:30 < Stee|> hah
22:31 < Stee|> so apparently my dance coach knew one of the dudes that practically invented bioinformatics
22:31 < Stee|> (according to him)
22:31 < kanzure> "bioconjugation" can't we just call this molecular conjugation -_-
22:32 < Stee|> http://www.adrianscott.com/ this guy
22:33 < kanzure> yashgaroth: so, what about a scheme where library items have lots of repetition (restriction sites etc.); you endonucleate the molecule; then you cap the oligos with something
22:34 < kanzure> and this 'something' has a special chemistry that allows it to combine with a chemically 'capped' growing oligo downstream
22:35 < yashgaroth> that seems tricky, but you're basically doing traditional synthesis with oligos instead of monomers
22:35 < kanzure> i guess this is just wishful thinking on my part, i should study the capping chemistry
22:35 < kanzure> correct
22:35 < kanzure> actually, that might not be necessary
22:36 < kanzure> as long as you can chemically modify the dna to have sticky ends again
22:36 < kanzure> *the oligos
22:37 < yashgaroth> you say that
22:37 < kanzure> ?
22:37 < yashgaroth> as if it's easy to accomplish
22:38 < yashgaroth> man my specialty is at the level of already having something vaguely resembling the gene you want
22:39 < delinquentme> WOAH.
22:39 < delinquentme> 29 new jobs on indeed for "bayesian"
22:39 < yashgaroth> they're all for bayesian chefs though
22:40 < kanzure> yashgaroth: ?
22:40 < kanzure> your specialty?
22:40 < yashgaroth> my interest and training
22:41 < kanzure> i don't get it. yes there are a few genes that i am interested in,
22:41 < kanzure> but it's easier to just order those genes over the web than building a dna synthesis device
22:41 < yashgaroth> over the web or from genomes I can harvest
22:42 < yashgaroth> and I still think the FBI will be all up in your anus if you have a dna synthesizer with any capability
22:43 < kanzure> "freedom of speech, 'cept i'm speaking in the language of life"or something
22:43 < kanzure> i could just encode my genome in everything and claim they are messing with my child
22:43 < kanzure> (kidding)
22:44 < yashgaroth> saying the botulinum coding sequence won't land you in prison, but printing it is a different story
22:45 < yashgaroth> though of course if you had primers, c. botulinum is a ubiquitous soil bacterium anyway
22:45 < kanzure> ok so because i'm allowing these bacteria to grow in my yard, i'm a criminal now?
22:45 < kanzure> come on
22:45 < yashgaroth> hey, I'm just saying the FBI is myopic
22:45 < Stee|> nah, wouldn't be the fbi
22:45 < kanzure> you sound like you've bee buttraped a few times by the feds
22:46 < kanzure> *been
22:46 < Stee|> too esoteric for them
22:46 < yashgaroth> in my nightmares
22:46 < kanzure> bee buttrape is even worse
22:46 < Stee|> DHS maybe
22:47 < yashgaroth> true, they're probably running the bioterror shit now
22:47 < yashgaroth> whatever, feds
22:47 < kanzure> ok, what if the library items were still 6mers/5mers but were biotinylated to something that has a high affinity for whatever polymerase is in the pcr step ("replenish library supplies")
22:48 < kanzure> er, or streptavidin not biotin
22:49 < yashgaroth> well, it'd be affinity to a ligase
22:49 < kanzure> there's multiple pcrs going on here
22:49 < kanzure> one for "make more library molecules"
22:49 < kanzure> another for "extension/ligation stuff"
22:50 < kanzure> maybe replenishing is not important.
22:51 < yashgaroth> that'd be easy compared to the actual extension
22:52 < kanzure> huh? pcr of 6mers is supposedly problematic- i've never tried it
22:52 < kanzure> in fact, i think i've only ever done pcr of at least 80+ bp sequences
22:52 < yashgaroth> oh, straight pcr would be impossible
22:52 < kanzure> wait what about single molecule pcr methods
22:53 < yashgaroth> same principles apply
22:53 < kanzure> that it's impossible? o.o
22:54 < yashgaroth> yes, single molecule pcr is mostly for analyzing single cells
22:54 < kanzure> please explain
22:54 < kanzure> oh is single molecule pcr talking about a single polymerase. duh. i should know this..
22:54 < yashgaroth> if you have a single template molecule, you can amplify any amount of product from it, it just takes more time/is harder to pull off
22:55 < yashgaroth> since you're going 1-2-4-8 instead of 1000-2000-4000
22:55 < yashgaroth> pacbio does their thing with single molecules, but that's sequencing
22:55 < kanzure> nonono there are many template molecules, they are just super short
22:57 < yashgaroth> if you had a way to make the polymerase synthesize an oligo that wasn't attached to the primer, you could melt it off and make more
22:58 < yashgaroth> like okazaki fragments, only they read the same site and length every time
22:58 < delinquentme> MY
22:58 < delinquentme> EYEBALLS
22:58 < delinquentme> ARE
22:58 < delinquentme> DRY
22:58 < delinquentme> yashgaroth, 0 FYI
22:58 < delinquentme> lol
22:58 < yashgaroth> ha, I knew you were high
22:59 < yashgaroth> oh damn you beat me to it
22:59 < delinquentme> =]
22:59 < delinquentme> nah i got this really awesome lifeskill im working on
22:59 < delinquentme> called selective mania
22:59 < delinquentme> its like being MAnIC!
22:59 < delinquentme> but being in control of it
22:59 < yashgaroth> you mean coke?
22:59 < kanzure> good luck with the control part
22:59 < delinquentme> ok all im tired as balls and got
22:59 < delinquentme> investments!
22:59 < delinquentme> lolol
22:59 < delinquentme> <3
23:00 < kanzure> delinquentme: http://diyhpl.us/~bryan/papers2/neuro/Mania-like%20behavior%20induced%20by%20disruption%20of%20CLOCK.pdf
23:00 < delinquentme> lololol
23:00 < kanzure> also here's a transcranial magnetic stimulation induced switch into mania:
23:00 < kanzure> http://diyhpl.us/~bryan/papers2/neuro/Transcranial%20magnetic%20stimulation-induced%20switch%20into%20mania%20-%20a%20report%20of%20two%20cases.pdf
23:00 < delinquentme> kanzure, yeahh but thats genetic
23:00 < kanzure> magnetic stimulation?
23:00 < kanzure> oh, clock
23:01 < delinquentme> but I feel that im pretty well psychologically grounded
23:01 < delinquentme> however. that would be my cognitive bias
23:03 < kanzure> Yawning associated with orgasm appeared as a side effect of clomiprarnine treatment in a depressed patient and disappeared when treatment ceased (McLean, Forsythe, & Kapkin, 1983)
23:03 < kanzure> ah science. thank god people are studying these things.
23:07 < utopiah_> ELLPs http://www.salk.edu/news/pressrelease_details.php?press_id=540
23:08 < delinquentme> lololol
23:08 < delinquentme> on that bombshell GOOD NIGHT!
23:08 -!- delinquentme [~asdfasdf@c-98-236-11-148.hsd1.pa.comcast.net] has quit [Quit: Leaving]
23:18 < yashgaroth> hmm if you had a strand that looked like ==------ permanently attached to a bead at the left side, with the overhang as your 6mer's complementary sequence
23:19 < yashgaroth> and the double stranded DNA was recognized by a nicking enzyme that would separate off the newly polymerized 6mer
23:19 < yashgaroth> then you melt off the newly made 6mer, wash it out and collect it, then repeat
23:19 < kanzure> wash and collect means purification?
23:20 < yashgaroth> I dunno, you'd need to collect the oligo preferentially since the enzymes wouldn't be immobilized
23:20 < yashgaroth> or I guess a change in pH could get the enzymes to immobilize if they had a tag, then you wash it out
23:21 < kanzure> ok there might be a microfluidics thing to sort the enzymes by mass
23:21 < kanzure> like based on flow velocity/mass
23:21 < yashgaroth> but you might not need to purify since it'd just be oligos and dNTP monomers
23:21 < yashgaroth> ehhh a light-dependent binding tag would be easier
23:21 < yashgaroth> don't wanna complicate things
23:22 < yashgaroth> but take the enzyme at http://www.neb.com/nebecomm/products/productR0607.asp
23:22 < kanzure> binding tag between what?
23:22 < yashgaroth> the nicking enzyme and the polymerase, to bind them to your bead or the chamber
23:22 < yashgaroth> so you can just collect the new oligos
23:23 < yashgaroth> and I suppose if they escape you can just cook them until they stop working
23:24 < yashgaroth> or if you're lucky they can be permanently bound, as long as they can reach the DNA to do their thing
23:25 < yashgaroth> so take that enzyme I linked, all the immobilized DNA looks like its template on that page, with a 6mer overhang coming out the bottom right
23:25 < yashgaroth> the 6mer being whatever one of the thousands you want
23:26 < yashgaroth> pol comes in, adds the 6 complementary bases you want
23:26 < yashgaroth> then the nicking enzyme chops off the newly made 6mer, which should melt off at ~room temp anyway
23:26 < yashgaroth> repeat
23:27 < yashgaroth> actually you wouldn't need/be able to separate out the oligo after every generation, but that shouldn't matter
23:27 < yashgaroth> they just accumulate until you run out of dNTPs
23:28 < yashgaroth> as long as the nicking enzyme doesn't permanently block the pol from attaching, you're good to go
23:29 < yashgaroth> ok that's a lot of text, but I just thought it up so I'm getting it all out there
23:29 < kanzure> "The Launch Loop along with Hyde's StarBridge vertical space fountain, and Earl Smith's Texas Railroad iron belt but inept orbital mechanics, all were subjects I urged the National Commission on Space to explore, when I gave testimony back in 1985."
23:29 < kanzure> "(http://www.kestsgeo.com/1techconcepts/documents/geniefiles/gesp475.html in case someone here actually is interested beyond figuring where to put the fatal bullets) The NCS ignored it all. In trying to figure out why, I explored those concepts' weak points and eventually "
23:29 < kanzure> "saw why they were rejected. But after ruminating on it all for several years, I used their compnent memes along with other memes - like those of the rotating disk drives with which I was familiar in development work as a career -
23:29 < kanzure> "http://www.kestsgeo.com/3generalwriting/techpoetry/techpoetry.html and suddenly the essences of KESTS to GEO jelled in my mind, a transportation structure between the earth surface at the equator, encircling the earth in the form of a hoop anchored on the equator and "
23:29 < kanzure> "reaching GEO above the opposite side of the planet up in GEO, where it formed a walk on at the ground, walk off and stay in orbit in GEO, no rocket stage involved at all, making it very efficient."
23:30 < kanzure> "Electrically powered, eventually by solar power stations that it enabled economically built in GEO <handwavy stuff goes here>"
23:30 < yashgaroth> god damnit do you want me to design your 6mer generator or are you just going into space instead
23:30 < kanzure> yashgaroth: i was reading some email before i sleep
23:30  * kanzure reads backlog
23:31 < yashgaroth> I'll try and write it into something more coherent tomorrow
23:31 < kanzure> well i figure my lack of sleep is why i can't figure out a good way to berrate it
23:32 < yashgaroth> omg it's genius all that shit is now creative commons'd
23:33 < kanzure> so the nicking enzyme would float around with your oligos when you go down to do the pcr extension steps elsewhere?
23:33 < yashgaroth> you can do it all in the same place
23:33 < kanzure> same reaction or just the same reaction chamber
23:33 < kanzure> o.o
23:33 < yashgaroth> same chamber, reactions alternate between pol and the nicking enzyme
23:34 < yashgaroth> soon as pol exposes the nicking site, 6mer gets cleaved and melts off at the reaction temperature anyway
23:34 < kanzure> if it's the same chamber then you have your solid beads with the library template mixed in with your other beads for growing a new strand
23:34 < kanzure> the beads need to be separated so that you can return the library beads back safely
23:34 < kanzure> but this is a minor nitpick really
23:35 < yashgaroth> it's all one strand
23:35 < yashgaroth> I mean, you need one chamber per 6mer, but the reagents are the same for all the chambers
23:36 < yashgaroth> i.e. dNTPs and the two enzymes
23:36 < kanzure> i'm not communicating well
23:36 < kanzure> my previous set of messages was about there being two different sets of beads
23:36 < kanzure> you mentioned that you had the overhangs attached to some dna attached to a bead
23:37 < kanzure> this bead is from the library
23:37 < yashgaroth> well, the combining of the 6mers into a long strand happens after, but that's a different story
23:37 < yashgaroth> all the beads in one chamber have the same template
23:37 < kanzure> there are other beads in this magical and increasingly hypothetical device (for keeping your new strands etc.)
23:37 < kanzure> correct
23:37 < kanzure> another minor nitpick, but having lots of chambers is impractical because of valving constraints
23:38 < kanzure> so instead i recommend you think about it in terms of different droplets
23:38 < kanzure> water-in-oil droplet
23:38 < kanzure> each library droplet has a collection of n>=1 beads
23:38 < yashgaroth> chambers, drops, whatever
23:38 < kanzure> ok ok just making sure :P
23:38 < kanzure> the chemistry is the important part anyway
23:38 < yashgaroth> hey man I thought the microfluidics was sorted
23:38 < kanzure> which part
23:39 < kanzure> separating out nicking enzymes?
23:39 < yashgaroth> naw you don't need to do that
23:39 < kanzure> *nicking enzyme
23:39 < kanzure> ok what were you referring to
23:39 < yashgaroth> knowing which oligo comes from where
23:40 < kanzure> i'm really tired am i missing your question :x
23:40 < yashgaroth> if you've got...1296 droplets, being able to collect the 6mers you need from each one
23:40 < yashgaroth> that part, I guess
23:41 < yashgaroth> tbh I'd be better off with some sleep as well
23:41 < kanzure> it definitely needs to be a sequential process
23:41 < kanzure> so you'd collect the beads from the 800th droplet, copy you up some oligos, send the droplet back for storage
23:41 < kanzure> then send these oligos down to get ligated
23:42 < kanzure> after the ligation reaction is complete you're ready to do another round of ligation
23:43 < yashgaroth> that's one way, sure
23:43 < yashgaroth> okay I really with IRC had one of those collaborative drawing programs right now
23:43 < yashgaroth> wish*
23:44 < kanzure> ASCII ART
23:44 < kanzure> i'll start
23:44 < kanzure> -------------------------------------------------
23:44 < kanzure> ok your turn
23:45 < yashgaroth> let's play pong     |      o
23:45 < yashgaroth> really I should just sleep on it, then whip up something in mspaint when I'm at the FPLC
23:45 < utopiah_> yashgaroth: http://www.aviary.com
23:46 < kanzure> http://cosketch.com/Rooms/akrjmxs
23:46 < utopiah_> actually http://advanced.aviary.com/
23:47 < kanzure> good night world
23:48  * yashgaroth also sleeps
23:48 -!- yashgaroth [~yashgarot@cpe-24-94-5-223.san.res.rr.com] has quit []
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23:58 < kanzure> http://www.opensource.org/node/603 "Open Source Initiative is switching to a member-led governance. For that, it will need member"
23:58 < kanzure> "The OSI Board would be very grateful if you would complete the totally anonymous survey which will help us understand what attributes you would like from OSI membership in the future"
--- Log closed Mon Feb 06 00:00:58 2012