| --- Log opened Sun Feb 05 00:00:56 2012 | ||
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| kanzure | "Received 16 December 1968. Available online 17 July 2002" | 00:26 |
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| kanzure | riiight... | 00:26 |
| kanzure | http://tatoluis.ta.funpic.org/password18Septiembre.htm | 01:35 |
| kanzure | http://groups.google.com/group/sci.med/browse_thread/thread/0638bc14a2ed74a7 | 01:36 |
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| kanzure | http://okulweb.meb.gov.tr/06/20/306107/downloads/library%20%C5%9Fifreleri.txt | 01:50 |
| kanzure | some more http://literature-free.blogspot.com/ | 01:52 |
| kanzure | http://64.27.4.128/forum/index.php | 02:02 |
| 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? | 02:05 |
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| kanzure | http://www.databisnisekonomi.com/html/account/cn/2/ | 02:12 |
| 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 | 02:15 |
| kanzure | raw addresses with no passwords: http://soulofrain.wordpress.com/2011/10/05/ezproxy-list-no-password/ | 02:16 |
| kanzure | haha their tutorials are sad :/ http://blog.csdn.net/ananias/article/details/674089 | 02:18 |
| kanzure | ah here's a pretty active forum.. http://www.i-nobel.com/bbs/index.php | 02:22 |
| kanzure | "Subject: 98,752 Posts: 515,068" | 02:23 |
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| kanzure | i-nobel is pretty impressive | 02:59 |
| kanzure | "[EBooks] Springer-Progress in colloid and of Polymer Science - Series uploaded (about 80 books)" | 03:05 |
| 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 " | 03:06 |
| 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.. | 03:08 |
| JayDugger | Anyone else here practicing intermittent fasting? | 03:12 |
| kanzure | http://bbs.ok6ok.com/ seems to be the same thing | 03:19 |
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| kanzure | lots of recent logins here: http://bbs.hx95.com/simple/index.php?t101852.html | 03:57 |
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| kanzure | hi delinquentme | 04:57 |
| delinquentme | howdy kanzure | 04:58 |
| delinquentme | kanzure, how does a blastocyte differ from the magic of a blastocyst | 05:21 |
| kanzure | delinquentme: pm | 05:44 |
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| 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. | 06:26 |
| 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. | 06:28 |
| 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. | 06:30 |
| Mariu | depends on what someone finds important, some people might not trade their own life for quality and vice-versa | 06:36 |
| Mariu | sorry for the poor wording | 06:37 |
| Mariu | *depends which things are important for someone - maybe fixes it a little | 06:39 |
| uniqanomaly_ | foucist: http://ezproxy.free-webmaster-resources.org/ | 06:41 |
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| 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. | 06:57 |
| 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. | 06:59 |
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| jrayhawk | Do tell. | 06:59 |
| JayDugger | On which point? | 07:00 |
| jrayhawk | particular symptoms | 07:01 |
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| 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!) | 07:03 |
| 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. | 07:05 |
| jrayhawk | Fun fact about ketosis: you can tilt breathalyzers by about .02 BAC with it. | 07:06 |
| JayDugger | Heh. How fortunate I practiced reciting the alphabet in reverse. | 07:08 |
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| JayDugger | Carbohydrate fasting means how low an intake per day? | 07:09 |
| JayDugger | Say, in grams per day? | 07:09 |
| 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 | 07:10 |
| 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 " | 07:11 |
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| 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. | 07:12 |
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| jrayhawk | Ketosis is fascinatingly transformational; huge swaths of your expressed genetics change and basically every system in your body starts working more consistently. | 07:15 |
| 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. | 07:16 |
| 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? | 07:17 |
| jrayhawk | Weird. | 07:18 |
| JayDugger | No, now that I think, that happened the first, oh, three weeks of I.F., then just again today. | 07:18 |
| jrayhawk | You might play with probiotics; it's pretty easy to starve out strains in the gut and get weird effects as a result. | 07:19 |
| jrayhawk | Gut biota have a very very deep and complex relationship with the rest of the body. | 07:20 |
| JayDugger | That's a thought. | 07:20 |
| jrayhawk | So, like, kimchi, sauerkraut, yogurt from grass-fed cows, also potentially various supplements | 07:21 |
| JayDugger | Yuck, yuck, lactose-intolerant, and pills suit me fine. | 07:22 |
| 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? | 07:23 |
| jrayhawk | Even the less horrifying forms of grain-feeding have all sorts of negative nutritional effects on milk and meat. | 07:25 |
| 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. | 07:26 |
| 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. | 07:27 |
| jrayhawk | you're... afraid of colloids? | 07:28 |
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| JayDugger | Nope, just raw milk. I'd rather eat mud. | 07:29 |
| 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 | 07:30 |
| 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 | 07:31 |
| 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. | 07:32 |
| JayDugger | It tastes like fish food, Tetra flakes, in particular. | 07:33 |
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| jrayhawk | I used to have a childhood-derived horror of fish, but then I discovered that wild-caught fish are delicious. | 07:35 |
| jrayhawk | Similar thing with nuts, now that I think about it. | 07:36 |
| jrayhawk | I'm glad food quality is making a comeback. | 07:36 |
| delinquentme | JayDugger, you've eaten tetra flakes? | 07:38 |
| JayDugger | Yes, I've eaten Tetra flakes. | 07:39 |
| JayDugger | They taste just like they smell. | 07:39 |
| 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 | 07:40 |
| JayDugger | Not so much tricked, as the vendor spoke very little English, and I speak no Chinese. | 07:41 |
| JayDugger | He pantomimed a dog pretty convincingly, though. | 07:42 |
| jrayhawk | "you! american dog! buy my soy sauce and rice!" | 07:42 |
| jrayhawk | I guess I should say slow-cooked wild-caught fish are delicious | 07:46 |
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| 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 | 08:03 |
| klafka1 | what are tetra flakes? | 08:09 |
| jrayhawk | pelletized dehydrated algae | 08:10 |
| jrayhawk | plus other miscellaneous ingredients | 08:10 |
| jrayhawk | oh no wait, tetra is the mineral one, right | 08:11 |
| jrayhawk | durrr | 08:11 |
| 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 | 08:12 |
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| JayDugger | I think, increasingly, programming counts as a new literacy. | 09:31 |
| JayDugger | I wonder by analogy, literacy:programming::post-literate society:? | 09:32 |
| JayDugger | Poorly chosen syntax on my part.... | 09:32 |
| delinquentme | JayDugger, interesting bits | 09:53 |
| delinquentme | do you still look at dogs as pets? | 09:53 |
| delinquentme | or with that event were they stepped down a notch | 09:54 |
| kanzure | JayDugger: i think neil has argued enough to have won that literacy argument by ow | 09:59 |
| kanzure | *by now | 09:59 |
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| 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 | 10:31 |
| delinquentme | someone in the anti-aging crowd talked about it | 10:32 |
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| falmot_ | http://ansistego.sf.net/shrooms-8.txt | 10:40 |
| 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. | 10:41 |
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| Mariu | later everyone | 10:59 |
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| roksprok | does anyone have a suggestion for what microcontroller to use for an electrode array? | 11:28 |
| roksprok | would it be better to use something like an arduino or beagleboard or just avr chips | 11:29 |
| 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 | 11:30 |
| roksprok | i've done a couple arduino projects but thats about as far as i have gone | 11:31 |
| roksprok | have you found that its limiting you in anyway? | 11:32 |
| 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 | 11:33 |
| 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 | 11:34 |
| roksprok | so its not exactly what i have in mind | 11:35 |
| roksprok | but in general its similar in that its bidirectional and has 256 total electrodes | 11:36 |
| 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 | 11:39 |
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| delinquentme | roksprok, well if you're wanting to build big ass mcnasty robotics | 11:41 |
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| delinquentme | the _ONLY_ issue i had with an arduino | 11:41 |
| delinquentme | wait | 11:41 |
| delinquentme | 2 things | 11:41 |
| 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 | 11:42 |
| 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 | 11:44 |
| 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 | 11:45 |
| 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 | 11:46 |
| delinquentme | roksprok, forums are good | 11:47 |
| delinquentme | but IRC SOOOO much faster | 11:47 |
| roksprok | delinquentme: and probably better for beginners, as I wouldn't be clogging up a forum with newb questions | 11:48 |
| 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 | 11:49 |
| 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 | 11:50 |
| roksprok | i just started on irc and am already amazed at how much free knowledge is out there | 11:51 |
| delinquentme | roksprok, i just posted to FB about how it blows my mind | 11:54 |
| delinquentme | :D | 11:54 |
| 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! | 11:55 |
| roksprok | yeah its really amazing | 11:59 |
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| jrayhawk | okay what about eating a mokbortolan bunting | 12:32 |
| delinquentme | O_o | 12:45 |
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| kanzure | neat, an opml rss file | 16:30 |
| kanzure | http://feeds.sciencedirect.com/opml.xml | 16:30 |
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| kanzure | license file | 16:53 |
| kanzure | http://web.archive.org/web/20000302122142/http://www.web-editions.com/web_editions_license.pdf | 16:53 |
| kanzure | or here http://web.archive.org/web/20050218014837/http://www.web-editions.com/license.html | 16:56 |
| -!- Troletariat is now known as Omega | 16:57 | |
| 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? | 16:58 |
| yashgaroth | you would get several different ligated combinations | 17:01 |
| kanzure | hm the margins are 35% | 17:02 |
| yashgaroth | you'd be inserting the fragment in place of the region between the two sites on the plasmid that got cut | 17:03 |
| 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? | 17:04 |
| yashgaroth | is there another site in the MCS with compatible sticky ends with BstEII? | 17:05 |
| yashgaroth | also it really depends on the plasmid and the fragment | 17:06 |
| n_bentha | oh i don't think there is another compatible sites... | 17:07 |
| yashgaroth | yeah probably not but it was worth a shot | 17:07 |
| yashgaroth | well what's the plasmid? | 17:09 |
| n_bentha | pcambia309 | 17:10 |
| yashgaroth | 0390? | 17:12 |
| yashgaroth | it's very odd they'd have a second site for an enzyme that's already in the mcs | 17:15 |
| n_bentha | it's a modified version, yashgaroth | 17:17 |
| yashgaroth | you have a link to the sequence? | 17:18 |
| n_bentha | to the pcambia sequence? | 17:21 |
| yashgaroth | yuss | 17:21 |
| yashgaroth | at least the one where you found two Bst sites | 17:24 |
| n_bentha | http://www.ncbi.nlm.nih.gov/nucleotide/AF406991? | 17:25 |
| n_bentha | see? | 17:30 |
| yashgaroth | indeed | 17:30 |
| 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 | 17:31 |
| yashgaroth | or design primers to overhang your fragment that have a better enzyme site on them | 17:33 |
| yashgaroth | ^which would also allow you to not have to make sure the insert is in the proper orientation | 17:34 |
| n_bentha | ah ok | 17:35 |
| 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? | 17:37 |
| 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 | 17:38 |
| 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 | 17:41 |
| 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 | 17:42 |
| 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 | 17:43 |
| 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 | 17:44 |
| 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? | 17:45 |
| n_bentha | some* | 17:46 |
| yashgaroth | kanzure: but the oligos still have the sticky ends from whatever enzyme you use | 17:46 |
| yashgaroth | which limits your ability to synthesize a sequence of your exact choosing | 17:47 |
| kanzure | perhaps there's some other scheme :/ | 17:48 |
| n_bentha | oh i think it's t4 and t7 viruses | 17:48 |
| yashgaroth | oh you mean when they replicate their genomes? | 17:49 |
| n_bentha | yes, they form concatemers | 17:49 |
| 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." | 17:51 |
| 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? | 17:52 |
| yashgaroth | you're cutting your gene fragment with the enzyme, or is it in another plasmid that has flanking Eco sites? | 17:53 |
| 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 | 17:54 |
| 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... | 17:55 |
| n_bentha | yes, yashgaroth. (i'm not concerned about the functionality of the gene) | 17:56 |
| 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? | 17:57 |
| yashgaroth | kanzure: I'm not seeing how overlap pcr applies...you mean for ligating the single oligos together? | 17:58 |
| kanzure | yashgaroth: growing oligo will be attached to a bead | 18:14 |
| 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 | 18:36 |
| yashgaroth | what gene are you using and why? | 18:43 |
| n_bentha | secret | 18:47 |
| yashgaroth | heh I can respect that | 18:47 |
| n_bentha | don't want to get scooped! | 18:48 |
| n_bentha | but if you look up the plasmid, you can find out kinda what i'm doing w/ it | 18:55 |
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| 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 | 18:58 |
| kanzure | come back and visit sometime | 18:59 |
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| kanzure | can someone get me a dns server other than 8.8.8.8 and 8.8.4.4? | 18:59 |
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| kanzure | ah nevermind | 19:01 |
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| kanzure | "Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides" | 19:05 |
| kanzure | hmm | 19:05 |
| 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 | 19:08 |
| yashgaroth | but then, I'm perfectly happy splicing just genomic and/or commercially available sequences | 19:10 |
| kanzure | yashgaroth: http://www.springerlink.com/content/141730735j433414/ | 19:16 |
| 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 | 19:17 |
| kanzure | not fair.. they are synthesizing custom primers i think | 19:23 |
| yashgaroth | it does look that way | 19:24 |
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| 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 | 19:27 |
| kanzure | so.. why do they think oligo synthesis /plus/ extension pcr /plus/ all these other steps are worthwhile? | 19:28 |
| yashgaroth | looks like that paper's more for library generation than gene synthesis | 19:30 |
| 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 | 19:31 |
| kanzure | i should go read some sloning stuff. i thought slonomics corp solved a bunch of these issues | 19:32 |
| kanzure | http://www.biotechniques.com/multimedia/archive/00003/BTN_A_000112953_O_3841a.pdf | 19:34 |
| 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" | 19:37 |
| 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 | 19:38 |
| kanzure | *10.5 bp/hr | 19:39 |
| kanzure | phosphoramidite synthesis is ostensibly faster | 19:39 |
| yashgaroth | oh it totally is | 19:40 |
| yashgaroth | on both points | 19:40 |
| Stee| | y'all use qiqqa, right? | 20:15 |
| yashgaroth | programs similar to it | 20:18 |
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| yashgaroth | hmm android app and character recognition, looks pretty snazzy | 20:20 |
| Stee| | auto-ocr | 20:24 |
| Stee| | auto-sync | 20:24 |
| Stee| | markup | 20:24 |
| yashgaroth | soo who feels like getting me a copy of http://online.liebertpub.com/doi/abs/10.1089/hum.2011.102 ? | 20:30 |
| Stee| | gimme a few | 20:31 |
| yashgaroth | HGT used to have a policy of the current issue being free, but then they became dicks | 20:31 |
| * 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 | 20:46 |
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| 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 | 20:47 |
| delinquentme | but its a tangent | 20:48 |
| 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 | 20:49 |
| 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 | 20:50 |
| delinquentme | nope i dont think thats chiral | 20:51 |
| delinquentme | like heres a thought statement | 20:51 |
| delinquentme | nm | 20:51 |
| * delinquentme ponders | 20:51 | |
| delinquentme | OHHHHH | 20:52 |
| yashgaroth | on a scale of 0 to whooooa maaaan, how high are you right now | 20:52 |
| 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 | 20:53 |
| delinquentme | whats the ship say in hitch hikers guide | 20:54 |
| delinquentme | "normality restored" ? | 20:54 |
| delinquentme | yashgaroth, srsly i was about 4 seconds from a nobel science prize in my mind | 20:58 |
| yashgaroth | heh | 21:00 |
| 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" | 21:07 |
| yashgaroth | ehh that's basically how it's pronounced anyway | 21:08 |
| delinquentme | prerogative | 21:09 |
| yashgaroth | yeah but no one ever says the first 'r' | 21:09 |
| delinquentme | ok cool so im not nuts | 21:17 |
| 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 | 21:18 |
| 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 | 21:19 |
| yashgaroth | well, sex and death are the two drivers of psychology | 21:20 |
| 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 | 21:22 |
| 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 | 21:23 | |
| 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? | 21:28 |
| Stee| | wonder if I could get an rss feed of science exchange | 21:29 |
| yashgaroth | I wish they'd have more than a 2 sentence description | 21:30 |
| 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 | 21:31 |
| 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 | 21:32 |
| 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 | :| | 21:33 |
| 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 | 21:34 |
| 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) | 21:35 |
| 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 | ^^^^^ | 21:36 |
| 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 | 21:37 |
| 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 | 21:38 |
| 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 | 21:42 |
| 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? | 21:43 |
| 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? | 21:44 |
| 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 | 21:45 |
| 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? | 21:46 |
| 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 | 21:47 |
| yashgaroth | it's the FBI dude, apparently that's all they can manage | 21:48 |
| delinquentme | lady replied! | 21:49 |
| 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 | 21:50 |
| delinquentme | ach | 21:51 |
| delinquentme | feels like http://nooutcasts.org/wp-content/uploads/2010/05/neo-wakes-up-within-the-matrix.jpg | 21:52 |
| 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 | 21:53 |
| -!- Mok_Away is now known as Mokstar | 21:54 | |
| 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 | 21:55 |
| 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? | 21:56 |
| 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 | 21:57 |
| 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 | 21:58 |
| Mokstar | "That ain't no cougar, that's a lioness!" | 21:59 |
| 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! | 22:00 |
| kanzure | neat, "Simultaneous measurements of the flow velocities in a microchannel by wide/evanescent field illuminations with particle/single molecules" | 22:05 |
| 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? | 22:06 |
| delinquentme | AH! | 22:07 |
| kanzure | delinquentme: noble gases | 22:07 |
| yashgaroth | some noble gases have been fluoridated | 22:09 |
| Mokstar | insults don't work on the noble gases, they just don't react | 22:09 |
| delinquentme | :D | 22:10 |
| 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 | 22:17 |
| Mokstar | how does this work? http://www.cnn.com/2011/TECH/innovation/03/04/mobile.microscope.ozcan.malaria/index.html | 22:18 |
| 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 | 22:19 |
| yashgaroth | in fact just resist arrest until you're schwarzenegger | 22:20 |
| delinquentme | LOLOL | 22:22 |
| delinquentme | but no really the punching method words | 22:22 |
| 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 " | 22:23 |
| 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 | 22:24 |
| 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 :( | 22:25 |
| 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 | 22:26 |
| 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 | 22:27 |
| 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 | 22:28 |
| 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 | 22:29 |
| kanzure | how about bgi? you might have to go to china though | 22:30 |
| Stee| | hah | 22:30 |
| 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 -_- | 22:31 |
| Stee| | http://www.adrianscott.com/ this guy | 22:32 |
| 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 | 22:33 |
| kanzure | and this 'something' has a special chemistry that allows it to combine with a chemically 'capped' growing oligo downstream | 22:34 |
| 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 | 22:35 |
| kanzure | as long as you can chemically modify the dna to have sticky ends again | 22:36 |
| kanzure | *the oligos | 22:36 |
| yashgaroth | you say that | 22:37 |
| kanzure | ? | 22:37 |
| yashgaroth | as if it's easy to accomplish | 22:37 |
| yashgaroth | man my specialty is at the level of already having something vaguely resembling the gene you want | 22:38 |
| delinquentme | WOAH. | 22:39 |
| delinquentme | 29 new jobs on indeed for "bayesian" | 22:39 |
| yashgaroth | they're all for bayesian chefs though | 22:39 |
| kanzure | yashgaroth: ? | 22:40 |
| kanzure | your specialty? | 22:40 |
| yashgaroth | my interest and training | 22:40 |
| 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 | 22:41 |
| yashgaroth | and I still think the FBI will be all up in your anus if you have a dna synthesizer with any capability | 22:42 |
| 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) | 22:43 |
| yashgaroth | saying the botulinum coding sequence won't land you in prison, but printing it is a different story | 22:44 |
| 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 | 22:45 |
| 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 | 22:46 |
| 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") | 22:47 |
| kanzure | er, or streptavidin not biotin | 22:48 |
| 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" | 22:49 |
| kanzure | maybe replenishing is not important. | 22:50 |
| yashgaroth | that'd be easy compared to the actual extension | 22:51 |
| 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 | 22:52 |
| yashgaroth | same principles apply | 22:53 |
| kanzure | that it's impossible? o.o | 22:53 |
| 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 | 22:54 |
| 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 | 22:55 |
| 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 | 22:57 |
| 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 | 22:58 |
| 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 | 22:59 |
| 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 | 23:00 |
| delinquentme | but I feel that im pretty well psychologically grounded | 23:01 |
| delinquentme | however. that would be my cognitive bias | 23:01 |
| 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. | 23:03 |
| utopiah_ | ELLPs http://www.salk.edu/news/pressrelease_details.php?press_id=540 | 23:07 |
| 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] | 23:08 | |
| 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 | 23:18 |
| 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? | 23:19 |
| 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 | 23:20 |
| 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 | 23:21 |
| 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 | 23:22 |
| yashgaroth | and I suppose if they escape you can just cook them until they stop working | 23:23 |
| yashgaroth | or if you're lucky they can be permanently bound, as long as they can reach the DNA to do their thing | 23:24 |
| 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 | 23:25 |
| 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 | 23:26 |
| 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 | 23:27 |
| yashgaroth | as long as the nicking enzyme doesn't permanently block the pol from attaching, you're good to go | 23:28 |
| 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." | 23:29 |
| 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 | 23:30 | |
| 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 | 23:31 |
| yashgaroth | omg it's genius all that shit is now creative commons'd | 23:32 |
| 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 | 23:33 |
| 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 | 23:34 |
| 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 | 23:35 |
| 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 | 23:36 |
| 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 | 23:37 |
| 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 | 23:38 |
| 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 | 23:39 |
| 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 | 23:40 |
| 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 | 23:41 |
| kanzure | after the ligation reaction is complete you're ready to do another round of ligation | 23:42 |
| 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* | 23:43 |
| kanzure | ASCII ART | 23:44 |
| kanzure | i'll start | 23:44 |
| kanzure | ------------------------------------------------- | 23:44 |
| kanzure | ok your turn | 23:44 |
| 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 | 23:45 |
| kanzure | http://cosketch.com/Rooms/akrjmxs | 23:46 |
| utopiah_ | actually http://advanced.aviary.com/ | 23:46 |
| kanzure | good night world | 23:47 |
| * yashgaroth also sleeps | 23:48 | |
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| 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" | 23:58 |
| --- Log closed Mon Feb 06 00:00:58 2012 | ||
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