2013-07-02.log

--- Log opened Tue Jul 02 00:00:13 2013
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nmz787_paperbot: http://journals.sfu.ca/rncsb/index.php/csbj/article/download/csbj.201304003/27101:19
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/f2c5005dd99d30dd7f38e07214cb91b0.pdf01:19
nmz787_'The biological microprocessor, or how to build a computer with01:19
nmz787_biological parts'01:19
nmz787_"Systemics, a revolutionary paradigm shift in scientific thinking, with applications in systems biology, and synthetic01:20
nmz787_biology, have led to the idea of using silicon computers and their engineering principles as a blueprint for the engineering of a01:20
nmz787_similar machine made from biological parts. Here we describe these building blocks and how they can be assembled to a general01:20
nmz787_purpose computer system, a biological microprocessor. Such a system consists of biological parts building an input / output01:20
nmz787_device, an arithmetic logic unit, a control unit, memory, and wires (busses) to interconnect these components. A biocomputer can01:20
nmz787_be used to monitor and control a biological system."01:20
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eleitlpaperbot: http://dx.doi.org/10.1016/j.theriogenology.2008.11.00502:33
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/9a4cf4bf851a85a22d956075bbb6c77c.txt02:33
@archelshoi eleitl02:34
@archelshttp://turingbirds.com/temp/1-s2.0-S0093691X08007784-main.pdf02:35
eleitlHi archels -- can you access that journal?02:35
eleitlAh, that was just a test paper.02:36
eleitlPaperbot doesn't seem to be able to.02:36
@archelsyep, I have access02:37
eleitlInstitutional?02:37
@archelsnod02:38
eleitlAs a matter of personal favor, I might have to ask you for some articles in future.02:38
@archelssure02:38
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eleitlWe're about to form a startup, and evaluating what particular biological system to cryopreserve.02:39
@archelsthis is an offshoot of that lab space you guys were setting up?02:40
@archelsI thought you were working on cryopreserving L. stagnalis02:40
eleitlYes.02:40
eleitlSorry, phone.02:42
eleitlNo, the L. stagnalis is a project which is difficult to get investors to pay for.02:42
eleitlWe'll probably try to weaselt that in via way of nonprofit, via donations.02:42
eleitlWe have a first internal round of investors which are interested in human cryopreservation, but can't pay for it all, especially if it's not a sustainable business.02:43
eleitlFirst funding round is small just about 55 kEUR, for the first 12 months.02:44
@archelsah. This is focused at advancing the necessary technology, rather than actually setting up long-term human cryo storage?02:44
eleitlWe do aim for a provider in Switzerland, but that's more long-term.02:45
eleitlOur first priority is to start cryopreserving something already useful, and produce enough results to be able to raise a lot more money in the second round.02:46
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eleitlWe're investigating several potential candidates, but unfortunately this is all for-profit business plan, so hush-hush.02:47
@archelsI guess the return-on-investment on fundamental research cannot be expected to be very high02:48
eleitlIt's more a teaser, to raise serious cash in the second round.02:48
@archelsright02:48
eleitlWe do have some interesting candidates, but research is intrinsically uncertain. You can work 1-2 years and only run into a wall.02:49
eleitlWe're going to have a specific exit clause in the contract in case we run into a wall.02:49
@archelssure, but cryopreservating is already a commercially successful business, so you're not starting from square one02:50
@archelsunless you're planning on doing something radically different02:50
eleitlyes, we're trying to improve existing methods, or we're trying to do something reasonably radical02:50
eleitlso we'll spend next 2-3 months reading papers, trying to figure out where our chances are better02:51
eleitlcurrently there are 3 options, ideally I want to have a few more02:51
eleitlwhat would you try to do if you were me?02:52
@archelsbeats me, I have no intuition for business =)02:53
@archelsgenerally I would argue for doing one thing and doing it well, but if you're just working up towards attracting more capital, then doing a few things in parallel could be beneficial02:54
@archelsbecause it gives you more things to show to potential investors02:55
eleitlwe will be focusing on one thing, but we try it to be the right thing02:55
eleitlif you want to raise, say 1-10 MEUR in the next round it better be something slightly exciting02:56
@archelsnot sure what is a reasonable target given 55k€ and 12 months02:59
eleitlI hesitate to say more, as archives are public03:00
eleitlwe have something hot, but quite uncertain03:01
eleitlif we go that route, 12 months will be just getting competent with that system03:01
eleitlif results are not a total failure, you can prolong the phase, or up the ante03:01
eleitlit might make sense to become a licensed animal research facility03:02
eleitlI understand it's easier if you order animals from a commercial supplier, and don't hold them longer than 12 hours in your research facility03:03
eleitlthis is US law, it might be different in the EU03:03
eleitlslaughterhouse is easy, but not really reproducible03:03
@archelshum, how fresh is the tissue you can get from there, anyway?03:07
eleitlif you pick it up yourself, very fresh03:08
@archelshope you have one nearby the lab, then :)03:09
@fenncats and dogs seems like a reasonable place to start; there's demand for it after all03:09
@fennmice are convenient03:09
eleitlin case of slaughterhouse, it will be pigs and cows03:10
@fennbut they are so big03:10
eleitlin case of commercial animals, rabbits or tats03:10
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eleitlbig is a plus, actually03:10
@archels.wa volume of pig brain03:12
yoleauxpig brain: amount: 3 oz (ounces): serving volume: (data not available); Physical properties: mass: 3 oz (ounces)03:12
@archelscanhazmetric?03:12
@fennyum yum03:12
@fennthat was serving size from a food database03:12
eleitlunfortunately, brains are not transplanted, and slaughterhouse methods tend to ruin your brain03:12
eleitlremoving the brain is also very difficult, and time-consuming03:13
@fenni dont suppose you could get dead dolphins03:14
eleitleven fixated brains are difficult, needle-nose pliers removing pieces of skull, etc.03:14
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eleitlI see no point in dolphins, and in general I'd rather stay away from the smarter critters03:14
@archelsso pigs about 0.1L, compared to human ~1L?03:14
@archelsdolphins, haha03:15
eleitlin case of brains, I would still like to look at snails03:15
eleitlbut, sales proposition to investors: zero03:15
eleitlditto whole body transplants, for that matter03:16
@fennlooks like a pig brain is 180g03:16
eleitlI'd hate working with live pigs03:16
@fennfrom http://mste.illinois.edu/malcz/DATA/BIOLOGY/Animals.html03:17
@fennmountain beaver?03:17
@archelseleitl: I take it you've considered rats?03:17
@archelsnot sure what you're trying to do; if working on perfusion methods then small brains like these are probably useless03:18
eleitlyes, in case we go animal research route rats and rabbits03:18
eleitlbut, first year we'll be doing fresh cadaver tissue03:18
eleitlstrictly no live critters on the premises03:18
@archelsexcept for the scientists03:18
eleitlwas thinking that as well ;)03:19
eleitlhuman research is less regulated, probably03:19
eleitlsacrifice a few lab assistants...03:19
eleitlnobody going to notice...03:19
gradstudentbotHave you read this paper?03:19
@archelsI think we got ourselves a volunteer03:21
eleitlcodo derecho se objetiva fractura de cupula radial <- fracture of the radial head03:26
eleitlcorrect?03:26
eleitlhttp://qz.com/99413/first-ever-human-head-transplant-is-now-possible-says-neuroscientist/03:26
heath http://www.bu.edu/abl/publications.html03:30
heath.title03:30
yoleauxBoston University: Collins Lab03:30
heathpublications from the lab03:30
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nmz787_paperbot: http://www.sciamdigital.com/index.cfm?fa=Products.ViewIssuePreview&ISSUEID_CHAR=E94E8DBF-C927-4DCD-B32C-221B7832ABB&ARTICLEID_CHAR=AB980A62-605D-4562-8CA1-360E43FA13104:15
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/dfa8eec7860d311a26224758562e0d10.txt04:15
nmz787_paperbot: http://solidstate.um.ac.ir/parameters/solidstate/filemanager/Scientific.American.Special.Edition.1997-12_Solid_State_Century.pdf04:21
paperbotConnectionError: [Errno 110] Connection timed out (file "/usr/local/lib/python2.7/dist-packages/requests/models.py", line 625, in send)04:24
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@ParahSailinwasted 15 minutes because i pasted a command where - was replaced by –08:37
@ParahSailinfucking code point U0x201308:38
chris_99yeah that's a PITA08:40
@kanzureit seems my phone is unable to charge unless i am directly staring at it08:41
@kanzuresomething about the micro usb connection not making full contact when i am not looking08:41
@kanzureand rebooting changes the charge from 2% to 40%08:44
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balrogkanzure: ya there?09:26
@kanzuremaybe09:27
balrogwanna add support for IOP to pdfparanoia?09:27
balrogI can provide a sample09:27
@kanzurebalrog: https://github.com/kanzure/pdfparanoia09:27
@kanzurei think iop is already supported09:28
@kanzureor there is an open bug report09:28
balrogalso the version in pip is busted09:28
@kanzureah, iop is not supported09:28
@kanzurewhy is it busted?09:28
balrog--verbose doesn't work09:28
balrog-o doesn't work09:28
@kanzurecan you fix? :(09:28
@kanzurei am really busy right now09:28
balrogit doesn't specify pdfminer as a prereq09:28
balrogah :|09:28
@kanzurepdfminer is not a prerequisite09:28
@kanzureoh wait, it is09:29
@kanzurehttps://github.com/kanzure/pdfparanoia/blob/master/requirements.txt09:29
balrogIOP seems to be "strip first page if contains certain text"09:30
balrogof course there may be additional watermarks09:30
@kanzuresure09:31
@kanzureone of the other plugins does that right now09:31
gradstudentbotFriends don't let friends go to super school.09:31
@kanzurebut it has a lot of checks09:31
balrogalternatively the ip and timestamp could be removed09:31
@kanzurebecause stripping the first page when it's not iop would be deadly09:31
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balrogI wonder if a becton-dickinson facscalibur PCI interface card would be of use to anyone09:39
balrogI don't have any other hardware or software09:39
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@ParahSailinany way to write "def derp(x): return (x, dict())" as a lambda or is this just language smell11:25
@kanzure[(x, dict()) for x in whatever]11:27
@kanzureoops, that's a list comprehension11:28
browniesheh11:28
browniesi think you have to be careful about when the dict() gets evaluated...11:28
@ParahSailinyeah thats the referential transparency thing that python lacks11:30
@ParahSailinis there list comprehension sugar for making itertools generators?11:32
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delinquentmekanzure, EYE MISS YEWWWW12:01
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@ParahSailincoworker is using ^I's for tabs instead of spaces; told to help him with project; time to quit12:59
@ParahSailinrepo master refuses to learn what pull request is on github; have to email diffs; time to quit13:05
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@kanzureParahSailin: why are you bothering13:10
@kanzure"Jonathan Rothberg has resigned from Life Technologies, amid Life's attempted $13.6 billion merger with Thermo Fisher Scientific.13:10
@kanzureRothberg's Ion Torrent business unit was cited by Thermo as a motivating factor behind the acquisition."13:10
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Burninatehttp://www.surgicalneurologyint.com/article.asp?issn=2152-7806;year=2013;volume=4;issue=2;spage=335;epage=342;aulast=Canavero;type=014:09
Burninateso Goertzel lives near me 0.o14:11
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@kanzureBurninate: i think he has a few kids. one is probably still in high school.14:19
Burninatehis face looks like someone I know the first name of, but not hte last14:20
Burninatein college14:20
Burninate*just graduated I guess14:20
@kanzurenot the amelious zarathustra one14:23
@kanzurethe other one14:23
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@kanzureReverse_dog: hi14:40
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@kanzuredoes anyone have recommendations for which sdr things to buy?14:40
@kanzuremaybe i should also pick something out from http://www.aircrack-ng.org/doku.php?id=compatibility_drivers14:42
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jrayhawk_broadcasting or receiving?15:06
@kanzurehow about both!15:07
@kanzurei just feel morally bad that i do not have this hardware laying around15:07
@kanzurei expect superkuh to have an idea or two except for whatever reason he is not actually here15:10
chris_99bladerf looks pretty nifty to me15:12
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balrogwhat was that zotero auto-import plugin?16:16
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@kanzurebalrog: zotero translators16:29
@kanzurebalrog: https://github.com/zotero/translators16:29
@kanzurebalrog: https://github.com/zotero/translation-server16:29
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superkuhpaperbot: http://proceedings.aip.org/resource/2/apcpcs/664/1/194_1?isAuthorized=no17:47
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/Ablative%20Laser%20Propulsion%3A%20A%20Study%20of%20Specific%20Impulse%2C%20Thrust%20and%20Efficiency.txt17:47
@kanzurei wonder if i am stripping out isAuthorized=no17:47
superkuhpaperbot: http://proceedings.aip.org/resource/2/apcpcs/664/1/194_117:48
paperboterror: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Ablative%20Laser%20Propulsion%3A%20A%20Study%20of%20Specific%20Impulse%2C%20Thrust%20and%20Efficiency.txt17:48
superkuhpaperbot: http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=APCPCS000664000001000194000001&idtype=cvips&doi=10.1063/1.1582108&prog=normal17:48
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/User%20Authentication.txt17:48
@kanzurearchels: maybe you have access?17:48
gradstudentbotI have to read all these articles.17:49
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streetyI think some selection process would be necessary17:56
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jonathan__how do I explain genetic algorithm seo optimization in order to pick the name of a new product, to a friend of mine who knows absolutely nothing about math or science and also thinks their opinion is usually the best...?18:18
jonathan__it's like explaining evolution to a catholic priest..18:19
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@kanzurejonathan__: i don't think genetic algorithms are the best way to do seo optimization. you should start from the other-end of the spectrum by looking at google search keyword tools that tells you how many people search for a given term.18:36
jonathan__sure, same thing18:36
jonathan__the reply I got back was something like "well I like my name better so what does it matter what other people think"   ... ummm yea18:37
jonathan__google adwords is just a manual simplistic way of doing genetic algorithm really18:38
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@kanzuregoogle adwords forces you to increase your margins so you can dump more of it into adwords18:43
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jonathan__oh, like cocaine.   "cocaine makes me work better.  so I can make more money.  so I can buy more cocaine.  so I can work better.  so I can make more money.  so I can buy more cocaine. ..."19:41
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jonathan__angelina jolie will now remove her ovaries to prevent future cancer. ...19:41
jonathan__so what body parts can I remove to reduce my cancer risk?19:42
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yashgaroththree, but you're not gonna like it19:43
jonathan__oh, says who?  maybe I enjoy self mutilation20:02
jonathan__let me see, my esophogus?20:03
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yashgarothhell if you go on soylent you can safely remove most of your digestive tract20:05
jonathan__i hope that stuff is tasty20:26
jonathan__i saw they were hiring for lab techs20:26
jonathan__to make the stuff..20:27
jonathan__yum!  cant wait to have my soylent chicken mcnuggets20:27
yashgaroth'lab tech' is a little optimistic20:27
jonathan__ok, factory worker20:28
yashgarothartisan manual labor20:28
jonathan__not so arty artisan20:29
jonathan__glorified stirring rod ok20:29
yashgarothI'm waiting for the choco-soylent20:29
jonathan__speaking of job opps I've now seen cybercoder ad for lead android engineer, listed $130K-$200K DOE20:30
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jonathan__now thats what i'm talkin bout yo20:30
jonathan__maybe that $200K is fake tho, I dunno20:30
jonathan__I dunno about soylent but I would love some hemp burger20:30
yashgarothmm, lentil steak20:31
jonathan__so there was a lab meetup today at 1pm20:31
yashgarothdamn I was busy for some reason20:31
jonathan__I was there at 1pm with some dude who came in off the street to help20:31
jonathan__but....   no you know who20:32
yashgarothlike literally just walked in?20:32
jonathan__new dude was basically sitting around staring at the wall while I attempted to revive my babies20:32
jonathan__some way to treat free labor  :-(20:32
jonathan__yea20:32
jonathan__well there was a carpenter dude there working on lab benches so lab was unlocked20:33
yashgarothI went and saw it on sunday, new benches have a distinct lack of ergonomics for people with legs20:33
jonathan__yea well, maybe you're just too tall  ha20:33
jonathan__evolve yourself20:33
yashgarothman you gotta put your knees somewhere20:33
jonathan__this is the era of downsizing20:33
jonathan__the lab will only be rented out to paraplegics20:34
yashgarothalso the display rack of big test tubes with colored liquid inside20:34
yashgarothI should make some skittles vodka in some of those for the opening20:34
jonathan__I'm gonna have a special treat for the opening day, wanna know what it is20:34
jonathan__oh it will be so cool20:35
jonathan__for me, anyway lol20:35
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yashgarothno don't tell me it'll be a surprise20:35
yashgarothyes20:35
jonathan__since I'm still the only one with an experiment, is that right?20:35
yashgarothteeeechnically20:35
jonathan__I mean, something actually living breathing bio with genes and stuff20:35
jonathan__"lets have a computer with fold it"  ummm come onnnnnn20:36
jonathan__that must be the "beyond" in btnb..  like, beyond believability that it will fly20:36
yashgarothkinda hard to start experiments when we still can't order shit to the lab address20:36
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jonathan__geez kind of hard to get work done in a meetup to do work if there's no one to direct the work, eh?20:37
gradstudentbotDropped my sample.20:37
jonathan__dropped the ball more like dude20:37
yashgarothyeah I mentioned to joseph that I'd be to the one next sunday and he was like 'oh yeah I just set up the repeating meetings'20:37
jonathan__presumably there's a work list, not20:38
jonathan__anyways I hope to turn a profit for the grand opening, that is MY measure20:38
yashgarothjob 1: make sure the machines go 'bing!' in time for opening day20:39
yashgarothor was it 'ping!' damnit we're screwed20:39
jonathan__i dunno what HIS measure is, maybe most number of rookies asking for help over and over?20:39
yashgarothwait are you gonna be selling wine at the opening or kombucha20:39
jonathan__my job 1:  measure progress via $$$ earned. period20:39
jonathan__what do you think..   I'm a friggin CAPITALIST cause I live in the U.S.A. not commie china20:40
yashgarothit's not usually my first, but until we can actually support the lab I'm okay with that20:40
jonathan__$$ just is a really good yardstick of success.20:41
jonathan__in this country, anyways20:41
yashgarothin pretty much any country, including china these days20:41
jonathan__not that the definition of success makes any sense.  other than that's what people want at the time.20:42
jonathan__the new dude today is apparently a yeast grower.20:42
jonathan__currently at a brewing supply co.20:42
yashgarothmaybe he just hadn't showered20:42
yashgarothoh20:43
jonathan__he was... fascinated...  by my  (your)  glassware20:43
jonathan__it made me somehow understand his career choices.20:43
yashgarothbrb buying lockbox20:43
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jonathan__gradstudentbot, do you know any hot postdocs?20:44
gradstudentbotYeah, but his project was so easy.20:44
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audy<3 gradstudentbot21:42
gradstudentbotWho has the latest version of the paper?21:42
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* brownies pokes gradstudentbot 21:53
gradstudentbotI think the centrifuge is broken.21:53
brownies.meow21:53
yoleauxhttp://moar.edgecats.net/cats/5NrgZ.gif21:53
heathhttp://parts.igem.org/Part:BBa_R005122:02
heathwhat does the SS AND DS acronyms stand for?22:02
heathi'm guessing DS = dna sequence?22:02
heathss = _ sequence22:02
yashgarothsingle and double stranded22:02
heathum, that makes complete sense22:03
* heath blushes'22:03
heathyashgaroth: do you know what OR1 and OR2 stand for?22:04
ParahSail1noccipital reticulin 1 and 222:04
yashgarothbinding sites for cI, apparently22:05
yashgarothor is that cl, damn alphabet22:05
yashgarothoh nope it's cI22:05
yashgarothso if the cI protein is being expressed in the cell, the promoter is repressed22:06
jonathan__bryan - about that paper you asked about, ultrasonic rug delivery22:08
heathParahSail1n: if you don't mind me askin,g how'd you know that? i'm trying to learn to put together my first assembly of these parts22:09
heathi'm reading the RFCs and also noticing that some of these parts aren't as well characterized as others have already pointed out22:10
ParahSail1ner, i just bs'd22:10
ParahSail1nyashgaroth's cro operon fits a lot better than my made up words22:11
yashgarothmy response was actually true but y'know whatever ignore me22:11
jonathan__I guess the question was about the driving circuitry.  well Im not sure why it takes a whole paper to describe differential signaling, anyways, it is relatively straightforward what they are doing, there is no need for an FPGA etc etc22:11
ParahSail1nin general, if you give two letters and a number for a gene, you're usually not going to have a useful time finding what that is without more context22:12
gradstudentbotThe paper got rejected.22:12
ParahSail1nso i didnt even bother googling22:12
yashgarothI thought it was just one of those technically correct answers22:13
jonathan__kanzure: so in essence just use a TI 6x DSP chip22:13
ParahSail1nhttp://www.uniprot.org/uniprot/?query=or1&sort=score 170 pages of or1 to choose from22:14
jonathan__the bigger problem is that the piezo element they created is 100% custom fabrication22:15
jonathan__can't get that off the shelf22:15
jonathan__also I thought that acoustic delivery systems had a habit of destroying whatever was being delivered22:17
jonathan__there's huge pressures at play, at micro sizes22:17
heathyashgaroth: heh, i'm sorry22:17
yashgarothno worries22:19
jonathan__It's a pretty meaty paper so I'd have to give it a more careful reading.22:19
heathslightly under the influence of things affecting my discernment :)22:19
jonathan__I just skimmed around here & there.22:19
jonathan__suppose you guys had 5 undergrads at your 100% disposal right now to work on whatever you want.  What would you have them work on?22:23
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heathdepends on their qualifications22:33
jonathan__I think I would have them work on cloning micheal jackson.22:34
heathi'm wondering which papers are associated with this guy: http://parts.igem.org/wiki/index.php?title=Part:BBa_J4500422:36
heathjonathan__: where are you located btw?22:36
heathkanzure: you know of anyone else here that's in the southeast?22:36
jonathan__i have no location, on a public channel22:37
* heath thinks he recalls TX22:37
heathhttp://www.amazon.com/Synthetic-Biology-Part-Volume-Characterization/dp/012385075422:37
heath.title22:38
yoleauxSynthetic Biology, Part A, Volume 497: Methods for Part/Device Characterization and Chassis Engineering (Methods in Enzymology): Chris Voigt: 9780123850751: Amazon.com: Books22:38
heathi want this22:38
heathhttp://libgen.info/view.php?id=72380822:38
heaththat works22:38
jonathan__oh, perfect, subject Техника22:40
jonathan__Hm let me file this under Техника22:40
jonathan__Техника: One morning, as Gregor Samsa was waking up from anxious dreams, he discovered that in his bed he had been changed into a monstrous verminous bug. He lay on his armour-hard back and saw, as he lifted his head up a little, his brown, arched abdomen divided up into rigid bow-like sections. From this height the blanket, just about ready to slide off completely, could hardly stay in place. His numerous legs, pitifull22:43
jonathan__in comparison to the rest of his circumference, flickered helplessly before his eyes.22:43
jonathan__That's one for the undergrads too.22:44
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yashgarothvery Техникаesque22:44
jonathan__yes quite22:45
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jonathan__many of the supposed projects I come up with are fine for undergrads or postdocs and often PI's claim it is worth pursuing, but the grad students, man they are never believers22:49
jonathan__ok maybe here's a better question22:50
gradstudentbotYou know they keep the mice in better conditoins than us.22:51
jonathan__what should the undergrads have to be experienced with in order to be valuable22:51
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jonathan__paperbot: http://www.wiley.com/WileyCDA/WileyTitle/productCd-1118610733.html23:01
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/b8435a6877fa587c45d8c700aa10b471.txt23:01
jonathan__max, I'm gonna need some of this  http://www.abmgood.com/APOE-siRNA-Lentivectors-7-APOE.html23:02
yashgarothdon't we all23:05
jonathan__paperbot http://www.nature.com/nrg/journal/v3/n10/pdf/nrg908.pdf23:07
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/a5e9fa2a7db16690a87bfcfcca66db31.pdf23:07
jonathan__do you know if that is really viable?23:08
yashgarothit's not really23:08
yashgarothRNAi has a lot of problems, lentiviruses have a lot of them too23:09
jonathan__"Abstract | RNA interference (RNAi) is a powerful approach for reducing expression of endogenously expressed proteins. It is widely used for biological applications and is being harnessed to silence mRNAs encoding pathogenic proteins for therapy. Various methods — including delivering RNA oligonucleotides and expressing RNAi triggers from viral vectors — have been developed for successful RNAi in cell culture and in vivo.23:10
jonathan__Recently, RNAi-based gene silencing approaches have been demonstrated in humans, and ongoing clinical trials hold promise for treating fatal disorders or providing alternatives to traditional small molecule therapies. "23:10
jonathan__so what's the problem?23:11
yashgarothmostly everything about it23:11
yashgarothpeople got all hyped because it was the first novel regulatory system discovered in a decade23:11
yashgarothto get use out of knocking down a gene, you'll probably need to knock it down in a significant fraction of the cells23:12
yashgarothlow duration of expression23:12
yashgarothand viral vectors are usually attacked by the immune system23:12
yashgarothin a few years it may play an important part in select therapies23:14
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jonathan__hmmmm23:15
yashgarothyou will often find that people who bank their entire academic career on a specific niche will be biased toward its relevancy23:15
jonathan__well sounds like regular injections are just required right23:16
jonathan__you know, bioshock style23:16
yashgaroththe advantage of gene therapy is theoretically that you only need one, or maybe a few injections23:16
yashgaroththere's some promising work in morpholinos, which are synthetic RNAi's with modified backbones that give them a much better half-life23:16
yashgarothsince the half-life of RNAi is absurdly short in vivo23:17
jonathan__well suppose that problem is solved...   lets say a microinjector is surgically sewn in like an insulin pump23:17
yashgarothnot recommended to take viral gene therapy without immunosuppressants23:18
yashgarothif you don't get the dose you need, you've immunized yourself against the medicine23:18
yashgarothit's hard to find a condition that's easily treated by RNAi alone, it's not like you often have Bad Gene X that if you could only turn it off you'd be fine23:20
yashgarothusually you just have two shitty recessive versions of Normal Gene X23:21
jonathan__paperbot http://www.tandfonline.com/doi/pdf/10.1081/E-EBAF-12004300223:22
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/8a72c68cef5e51ac07e4bcffccce4b44.txt23:22
yashgaroth"RNAi technology promising to create safe and effective models that may in fact reach the herds in the future" right23:22
jonathan__paperbot http://www.tandfonline.com/doi/abs/10.1081/E-EBAF-12004300223:22
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/d6bf4314aa10356701bbc9d4def39774.txt23:23
jonathan__ah you're such a pessimist23:24
yashgarothnah just accurate23:25
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jonathan__I read it in Nature, it has to be true!23:26
jonathan__paperbot http://www.annualreviews.org/doi/pdf/10.1146/annurev-biophys-083012-13040423:26
paperboterror: HTTP 200 http://diyhpl.us/~bryan/papers2/paperbot/b15aa335bb7be028b24757b21d4efe33.pdf23:26
yashgarothadd that one to gradstudentbot's cache23:26
gradstudentbotHey, does anyone have an extra undergrad?23:26
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jonathan__what happened to that journal supposed to be for publishing papers that don't work...23:28
yashgarothjournal of negative results? same thing that happened to everyone going to open access journals...'well not everyone's doing it so I'll look bad by publishing there'23:29
yashgarothmy impact factoru~~23:30
yashgarothoh you published in JNR? you must be terrible at experiments, unlike me who burns all results that don't fit my worldview/grant23:31
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jonathan__hm23:32
yashgarothI exaggerate for comedic and pessimistic effect, but not by much23:32
jonathan__"Use and abuse of RNAi to study mammalian gene function"23:33
jonathan__WG Kaelin - Science, 201223:33
yashgarothheh23:34
jonathan__My poor APOE23:35
jonathan__will never be silenced  :-(23:35
jonathan__paperbot http://www.nature.com/mt/journal/vaop/ncurrent/full/mt2013124a.html23:37
paperbotHTTP 401 unauthorized http://www.nature.com/mt/journal/vaop/ncurrent/pdf/mt2013124a.pdf23:37
jonathan__oh you just need to add NANO particles!23:38
jonathan__"Biodegradable Lipids Enabling Rapidly Eliminated Lipid Nanoparticles for Systemic Delivery of RNAi Therapeutics"23:38
jonathan__zzzzz23:40
yashgarotheurgh and also zzzz23:40
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--- Log closed Wed Jul 03 00:00:14 2013

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