| --- Log opened Wed Mar 28 00:00:10 2012 | ||
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| Vicarious | 'morning | 03:20 |
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| ThomasEgi | mornin | 03:23 |
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| cluckj | kanzure do you know anything about singularity U's synbio launchpad thing? | 07:47 |
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| audy | People are 3D printed by their mothers | 08:40 |
| Mokbortolan_1 | uhh | 08:43 |
| Mokbortolan_1 | no | 08:43 |
| Mokbortolan_1 | no they're not | 08:43 |
| * Mokbortolan_1 spergs out. | 08:43 | |
| archels | self-assembly, more like. | 08:45 |
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| ThomasEgi | modern dental tech is quite something..that broken off tooth of mine now looks better than it did befor it snapped | 08:54 |
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| Urchin | lol, I don't need much dentistry done, so I freaked out my new dentist first time I had to get some drilling done by requesting that she does that without anesthetics | 10:15 |
| n_bentha | masochist much? | 10:16 |
| kanzure | n_bentha: nope, just thoughtless :P | 10:17 |
| Urchin | lol, no | 10:17 |
| Urchin | it was a minor repair | 10:18 |
| Urchin | the anesthetic would be more trouble than it was worth | 10:18 |
| n_bentha | Ah. I see. | 10:18 |
| Urchin | I usually go to the dentist couple of times in a row every 5 or 6 years | 10:19 |
| Urchin | last time I went anesthetic injections were not given away for everything | 10:19 |
| Urchin | *before that time | 10:20 |
| Stee| | anaesthesia doesn't work on me, or at least the last one they used didn't | 10:21 |
| Stee| | so they used 12 shots of novacaine instead | 10:21 |
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| n_bentha | I'm really sensitive to anesthetics. | 10:22 |
| n_bentha | Alcohol is usually good enough for me | 10:22 |
| kanzure | n_bentha: but really. how did those transformations go? | 10:27 |
| kanzure | cluckj: yes i do | 10:27 |
| n_bentha | T_T | 10:28 |
| * n_bentha cries | 10:28 | |
| n_bentha | So they took up the original plasmid just fine. Had about 100 colonies on the kanamycin plate. | 10:28 |
| kanzure | did yashgaroth murder your culture | 10:29 |
| kanzure | ah | 10:29 |
| n_bentha | But the plasmid that I inserted my gene fragment into...none of the bacteria expressed resistance to kanamycin, and the plates were empty :O | 10:29 |
| n_bentha | Yeah, I think yashgaroth murdered them | 10:29 |
| audy | your kanamycin might've been super-kanamycin by accident | 10:31 |
| audy | did you grow them on non-kan plates as well? | 10:31 |
| cluckj | anything interesting, kanzure? | 10:34 |
| kanzure | cluckj: sure i have things to say about them.. | 10:34 |
| cluckj | haha | 10:35 |
| kanzure | i just woke up, can i rant at you later about them? | 10:35 |
| cluckj | yup | 10:35 |
| kanzure | i think the program is generally good but there's a few weird choices | 10:35 |
| kanzure | like, for instance, why in holy hell is eri gentry an advisor | 10:35 |
| kanzure | eri's startups haven't done much | 10:35 |
| cluckj | isn't she in charge of biocurious? | 10:40 |
| n_bentha | audy... | 10:41 |
| audy | n_bentha yep? | 10:42 |
| n_bentha | they grew on the kana plates just fine w/ the original plasmid...but not the plasmid that i inserted a gene fragment into | 10:42 |
| audy | which plasmid? | 10:42 |
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| n_bentha | one w/ a chemical inducible promote | 10:43 |
| audy | n_bentha E. coli? | 10:44 |
| n_bentha | Yup | 10:44 |
| audy | n_bentha do you have a link to the promoter spec? | 10:45 |
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| n_bentha | sorry, audy. i don't have one at the moment. | 10:52 |
| audy | n_bentha: It'd be weird but is the insert site in the kan-resistance gene? | 10:53 |
| n_bentha | I sure hope not! | 10:53 |
| n_bentha | I thought that might be the case. I wanted to try them w/ another antibiotic plate as well. | 10:54 |
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| Mokbortolan_1 | http://www.process.org/discept/2011/11/17/draco-death-to-the-virus/ | 11:24 |
| Mokbortolan_1 | Article about MIT research that could potentially spell the end of viral infections | 11:25 |
| kanzure | 1) that sounds a lot like hype to me | 11:25 |
| Mokbortolan_1 | claims, evidence, all that | 11:26 |
| Mokbortolan_1 | DRACO proved successful against all 15 viruses tested “including rhinoviruses that cause the common cold, H1N1 influenza, a stomach virus, a polio virus, dengue fever and several other types of hemorrhagic fever.” [2] | 11:26 |
| kanzure | oh, a caspase rna oligo | 11:26 |
| kanzure | hrmm | 11:26 |
| Mokbortolan_1 | right now it's produced in modified bacteria | 11:27 |
| n_bentha | thank for the 2011 article. this is 2012 btw | 11:28 |
| Mokbortolan_1 | uhh | 11:28 |
| Mokbortolan_1 | Nov. 2011 | 11:28 |
| Mokbortolan_1 | six months ago | 11:28 |
| n_bentha | Then how come I heard about it in august? | 11:29 |
| Mokbortolan_1 | 'cos the paper itself came out last July | 11:29 |
| kanzure | what? | 11:29 |
| n_bentha | Yea, so not 6 months ago. | 11:29 |
| Mokbortolan_1 | the article was 6mo ago | 11:29 |
| Mokbortolan_1 | so, would you prefer that I only talk about papers submitted in the last four months? | 11:30 |
| Mokbortolan_1 | err, published | 11:30 |
| n_bentha | that article and the paper it refers to were published at different times? | 11:31 |
| Mokbortolan_1 | yes | 11:31 |
| n_bentha | nevermind, i'm going to go yell at some undergrad. | 11:31 |
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| kanzure | nice | 11:31 |
| kanzure | n_bentha is legit | 11:31 |
| Mokbortolan_1 | I was going to suggest he put me on ignore to prevent the offense of his sensibilities in the future | 11:33 |
| kanzure | no i think he misinterpreted something | 11:33 |
| kanzure | /or/ one of his undergrads lied to him | 11:33 |
| Mokbortolan_1 | seems like pretty exciting research | 11:35 |
| Mokbortolan_1 | no idea why AIDS funders aren't all over this, or maybe they've been burned too many times in the past | 11:35 |
| kanzure | non-profits don't operate efficiently | 11:39 |
| Mokbortolan_1 | ohhhh | 11:39 |
| kanzure | they just have people send in grant proposals, and they may or may not choose it based on your pedigree or something | 11:39 |
| Mokbortolan_1 | I know why... this was the plot line from "I Am Legend" | 11:39 |
| Mokbortolan_1 | interesting comment on reddit, what would it do to people with inactive herpes infections? | 11:41 |
| Mokbortolan_1 | it would also completely stop this: http://www.panspermia.org/virus.htm | 11:47 |
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| kanzure | yashgaroth: his colonies diiied | 11:51 |
| kanzure | he is suing you for the damages | 11:52 |
| yashgaroth | them dying implies that they grew first | 11:52 |
| kanzure | uh | 11:52 |
| kanzure | uhh | 11:52 |
| yashgaroth | wait lemme read the logs | 11:52 |
| kanzure | no, they could survie without resistance, but they would be killed off soon | 11:52 |
| kanzure | *survive | 11:53 |
| Mokbortolan_1 | maybe that's what he was grumpy about | 11:53 |
| yashgaroth | oh it looks like the fragment insertion fucked up the resistance gene somehow | 11:54 |
| yashgaroth | at least his transformation of the original plasmid worked, which I imagine wasn't happening before, so I'm vindicated | 11:54 |
| kanzure | haha | 11:55 |
| katsmeow-afk | Mokbortolan , they aren't all over it because they make far more money selling lots of medicines that marginally might work, which you must keep on buying | 11:58 |
| yashgaroth | DRACO won't work for HIV, or any other virus with latency | 11:58 |
| katsmeow-afk | even if given continuously? | 11:59 |
| yashgaroth | you can probably get it below detectable levels, but it'd be far more expensive than the current small-molecule treatments | 11:59 |
| katsmeow-afk | why more expensive? they'll make the stuff in huge vats of bacteria | 12:00 |
| yashgaroth | GMP protocols for biologics is far more strenuous than for small-molecule | 12:00 |
| yashgaroth | the current HIV drugs are only expensive because they're recouping research costs | 12:01 |
| kanzure | and because you pay for them | 12:01 |
| yashgaroth | and because americans will pay a shit-ton for them, yes | 12:01 |
| kanzure | in cases other than STDs, for instance in rare diseases, there are many "cures" in the patent database, but there's all sorts of licensing costs if you want to sell it | 12:02 |
| kanzure | in many cases, you could just manufacture it yourself | 12:02 |
| kanzure | for much less. | 12:02 |
| yashgaroth | Myriad's BRCA test being the most obvious one | 12:02 |
| kanzure | actually, i haven't done a full review of this. i should probably publish instructions for some common things. | 12:02 |
| kanzure | yes, true | 12:02 |
| kanzure | but for instance: crohn's. | 12:03 |
| kanzure | there should probably be a site about this.. sometimes the rare diseases groups are too small to make a profit, but they are definitely large enough to support themselves with DIY methods | 12:03 |
| yashgaroth | sometimes the rare diseases can be the most profitable, e.g. Alexion | 12:04 |
| yashgaroth | $2mil per patient per year, with only a few dozen cases | 12:05 |
| kanzure | yeah, so, $2mil is more than enough to fund DIY stuff | 12:05 |
| kanzure | obv. patients get financial assistance for that, but there are some that will afford it | 12:05 |
| kanzure | there are a few blood diseases that cost >$1,000/week.. that would definitely be able to support a DIY ecosystem | 12:06 |
| yashgaroth | all the hemophilias | 12:06 |
| kanzure | i'm not familiar with them, really | 12:06 |
| yashgaroth | they're all hella expensive, from what I hear | 12:07 |
| kanzure | yes | 12:07 |
| kanzure | http://blogs.nature.com/spoonful/2011/09/soliris.html | 12:07 |
| kanzure | "you can expect to shell out more than $400,000 per year because that’s the price of the antibody drug that just received regulatory approval in the US to treat the clotting disease." | 12:07 |
| kanzure | ok.. $400k/year for an antibody? hahah | 12:07 |
| kanzure | an antibody project is totally doable | 12:07 |
| kanzure | "Atypical hemolytic-uremic syndrome (aHUS) is a life-threatening genetic disease affecting fewer than 1,000 Americans in which red blood cells break apart as they squeeze through small blood vessels leading to anemia, abnormal bleeding and kidney failure." | 12:08 |
| kanzure | " (The monoclonal antibody, which is directed against the complement protein C5, had been on the market since 2007 for the treatment of another rare blood disorder called paroxysmal nocturnal hemoglobinuria.)" | 12:08 |
| yashgaroth | antibodies cost maybe $1/mg to manufacture if you don't have to recoup clinical trial and research costs | 12:08 |
| kanzure | i don't expect antibody manufacturing facilities to cost more than.. $30-$50k | 12:08 |
| kanzure | especially in low volume | 12:08 |
| yashgaroth | well...with a nice stable cell line, you can get 5 grams per liter of culture | 12:09 |
| kanzure | by low volume i meant 1 person | 12:09 |
| yashgaroth | one liter of media costs 50 bucks | 12:09 |
| kanzure | but 1000 patients is already low volume :) | 12:09 |
| kanzure | well let's see how many grams in a dose | 12:10 |
| kanzure | 600-900 mg per week | 12:10 |
| kanzure | oh, 600-900 mg per week for the first few weeks, followed by 300-400 mg per week | 12:10 |
| yashgaroth | 10 mg/kg body weight, every 2 weeks, is a very rough average; it depends on the disease | 12:11 |
| kanzure | yeah, um. | 12:12 |
| yashgaroth | actually I'd say $0.1/mg is doable | 12:12 |
| yashgaroth | *with enough seed money to develop the stable cell line | 12:13 |
| kanzure | http://en.wikipedia.org/wiki/Hemolytic-uremic_syndrome | 12:13 |
| kanzure | what's that rare diseases website? | 12:14 |
| kanzure | curewithme? | 12:14 |
| kanzure | patientslikeme? | 12:14 |
| yashgaroth | no idea | 12:14 |
| yashgaroth | whyismyurineblue | 12:15 |
| kanzure | damn only 1 person on patientslikeme http://www.patientslikeme.com/conditions/1500 | 12:15 |
| kanzure | http://www.patientslikeme.com/search?q=hemolytic&commit=Search | 12:16 |
| kanzure | 10 people with autoimmune hemloytic anemia | 12:16 |
| kanzure | ah here's a non-profit.. http://www.atypicalhus.net/ | 12:18 |
| kanzure | haha.. "There is no cure for Atypical HUS. In fact, there is not a standard treatment, as each case is different. (Note : With the advent of Soliris, this may change over time)" | 12:19 |
| yashgaroth | "each case is no longer different" | 12:20 |
| kanzure | and 252 members here: http://atypicalhus.ning.com/profiles/members/ | 12:21 |
| kanzure | so, just pick someone and give them the pitch | 12:21 |
| kanzure | i bet you could get all of them to pitch in more than $100/mo.. so 25k/mo | 12:23 |
| yashgaroth | depends what percentage of them are already on insurance | 12:23 |
| kanzure | all of them. | 12:23 |
| kanzure | but often, people can spare $100/mo | 12:23 |
| kanzure | and you wouldn't be able to tap into their insurance money anyway | 12:23 |
| yashgaroth | true | 12:24 |
| delinquentme | le whut? | 12:25 |
| kanzure | delinquentme: many rare blood diseases have treatments that cost >$300k/year | 12:25 |
| kanzure | delinquentme: so the idea is to just do a DIY operation where they pitch in money not to buy medicine but to buy equipment or something | 12:25 |
| delinquentme | but dont they need the meds? | 12:26 |
| kanzure | they would use the equipment to make the meds | 12:27 |
| uniqanomaly_ | or die tryin | 12:28 |
| yashgaroth | it's like insurance insurance, in case their insurer decides to stop paying for whatever reason | 12:28 |
| kanzure | heh | 12:28 |
| kanzure | yashgaroth: it would be interesting to do this by bitcoin | 12:28 |
| delinquentme | uniqanomaly_, you're 50 cent? | 12:28 |
| uniqanomaly_ | delinquentme: sure | 12:28 |
| -!- uniqanomaly_ is now known as uniqanomaly | 12:28 | |
| uniqanomaly | 'sup | 12:29 |
| yashgaroth | bitcoins do seem to have stabilized a little | 12:29 |
| kanzure | i wonder if kickstarter would approve that sort of project | 12:29 |
| kanzure | prolly not. | 12:30 |
| yashgaroth | haha no | 12:30 |
| kanzure | i'm not sure why someone hasn't done this already | 12:35 |
| kanzure | let's say that a family can't get insurance, and has to pay $400k/year for this drug | 12:35 |
| kanzure | you can /easily/ bribe some researcher to work for $10-$20k/mo to produce the antibody | 12:36 |
| yashgaroth | they do subsidize in that case | 12:36 |
| kanzure | hm? | 12:36 |
| yashgaroth | alexion does | 12:36 |
| kanzure | so then what's the point of having insurance for that, then? | 12:36 |
| yashgaroth | making money | 12:36 |
| yashgaroth | oh you mean patients | 12:37 |
| kanzure | no, i mean, what is the incentive of the patient to have insurance to pay alexion | 12:37 |
| kanzure | yes | 12:37 |
| yashgaroth | insecurity of life, maybe | 12:38 |
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| Mokbortolan_1 | I had an idea that might be helpful with this stuff | 13:07 |
| Mokbortolan_1 | "public x prize", where goals and prizes are implemented by the public | 13:08 |
| Mokbortolan_1 | if it were international, then non-us organizations could potentially skirt patent issues | 13:09 |
| yashgaroth | sure, if you don't distribute the product in the US | 13:10 |
| kanzure | Mokbortolan_1: where does the prize money come from? | 13:12 |
| kanzure | most non-us organizations exist in countries that are signed onto WIPO, so they all believe in international patents | 13:13 |
| Mokbortolan_1 | kanzure: crowdsourced | 13:18 |
| Mokbortolan_1 | want to make a prize to develop a cheap cure for nodding disease? donate $5. There's a bit more to it in terms of prize criteria, award, and mobility of funds, but that's the basic idea | 13:19 |
| yashgaroth | prizes don't fund research though | 13:20 |
| yashgaroth | the space prize gave 10 mil for work that cost >100mil | 13:21 |
| kanzure | the space prize was all funded by insurance fraud anyway | 13:22 |
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| kanzure | Mokbortolan_1: i suggest you read up on knowledge eonomy international | 13:22 |
| kanzure | or whatever jamie love is doing these days | 13:23 |
| kanzure | http://diyhpl.us/wiki/transcripts/open-science-summit-2010/jamie-love-knowledge-ecology-international/ | 13:23 |
| kanzure | or the health impact fund | 13:23 |
| kanzure | http://diyhpl.us/wiki/transcripts/open-science-summit-2010/aiden-hollis-health-impact-fund/ | 13:23 |
| kanzure | there was also their q&a session.. http://diyhpl.us/wiki/transcripts/open-science-summit-2010/innovation-paradigm-qa/ | 13:23 |
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| kanzure | well this is weird.. http://keionline.org/node/1384 | 13:31 |
| kanzure | "Today India granted a compulsory license on patents held by Bayer on the cancer drug sorafenib. The Bayer price of INR 3,411,898 per year (69 thousand USD) is more than 41 times the projected average per capita income for India in 2012, shattering any measure of affordability." | 13:31 |
| kanzure | "he 62 page decision grants the CL for the life of the patent, and grants a 6 percent royalty, which was at the high end of the UNDP 2001 royalty guidelines." | 13:32 |
| kanzure | "Bayer tried to justify its high price by making claims of high R&D Costs, but refused to provide any details of its actual outlays on the research for sorafenib, a cancer drug that was partly subsidized by the US Orphan Drug tax credit, and jointly developed with Onyx Pharmaceuticals." | 13:32 |
| kanzure | "Onyx told the SEC that the cost of R&D, pre-Orphan Drug tax credit, was $275 million through the 2005 FDA approval of sorafenib, including outlays on other compounds, indications that were not approved for marketing, and for expanded access trials in the United States that had limited value as scientific experiments." | 13:32 |
| kanzure | "Because the facts in the Bayer case were extreme, the Controller was faced with a stark choice, and had the compulsory license been denied, the India statute on "reasonably affordable" pricing would have seemed like an empty protection for the public." | 13:33 |
| kanzure | "It would have been nice for the decision to acknowledge the several compulsory licenses on drugs and medical devices that were issued in Italy and the United States in recent years." | 13:33 |
| kanzure | http://keionline.org/node/862 http://keionline.org/node/1219 http://keionline.org/content/view/41/1 | 13:34 |
| kanzure | compulsory licensing. haha. | 13:34 |
| Mokbortolan_1 | yashgaroth: no, the prize targets would have to be crafted to be within an appropriate range | 13:38 |
| Mokbortolan_1 | I'm thinking of researchers working on their own or small teams funded by venture capitalists | 13:38 |
| Mokbortolan_1 | perhaps even just, "identify the pathogen that causes nodding disease" as a first step for that one | 13:39 |
| Mokbortolan_1 | that shouldn't take hundreds of millions to accomplish | 13:39 |
| kanzure | i wonder if a distributed DIY production capacity for these drugs, | 13:39 |
| kanzure | coupled with bitcoin and proper anonymization, | 13:40 |
| kanzure | could completely cut off their revenue. | 13:40 |
| yashgaroth | totally, but a prize implies you don't give the money out until there's a cure | 13:40 |
| Mokbortolan_1 | right | 13:40 |
| kanzure | then you can blackmail these multi-billion dollar pharma companies for a pay off | 13:40 |
| Mokbortolan_1 | I had ideas for how to structure it, like perhaps prize goals | 13:40 |
| yashgaroth | but if you don't stop after they pay you off, they come to kill you | 13:41 |
| kanzure | "Look, we're manufacturing enough to treat all 1000 of your patients. You're losing $400 million a year. Our cost of operations is $100k. You give us $100 mil, and we'll stop this." | 13:41 |
| Mokbortolan_1 | no they don't "come kill you", you just die accidentally, perhaps of a heart attack, or private airplane crash | 13:42 |
| kanzure | them subsidizing patients that don't have insurance, really puts a blocker on this | 13:43 |
| kanzure | but they are still getting paid *somehow* | 13:43 |
| yashgaroth | that's why you go for cancer drugs, insurance is more likely to skip those | 13:43 |
| kanzure | really? | 13:44 |
| kanzure | also: another soft-spot is in between "companies that have patented stuff that works" and "companies that aren't doing anything with their patents" | 13:44 |
| yashgaroth | this is why I prefer going after drugs that have an off-label enhancement effect, which insurance won't cover and the company won't develop for | 13:46 |
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| kanzure | oh neat: "TRIPs also provides that the requirements for a compulsory license may be waived in certain situations, in particular cases of national emergency or extreme urgency or in cases of public non-commercial use." | 13:48 |
| kanzure | http://en.wikipedia.org/wiki/Agreement_on_Trade-Related_Aspects_of_Intellectual_Property_Rights | 13:48 |
| kanzure | "The Doha declaration allows compulsory licenses to be issued in developed countries for the manufacture of patented drugs, provided they are exported to certain countries (principally, those on the UN's list of least-developed countries and certain other countries having per-capita incomes of less than US$745 a year)." | 13:49 |
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| ParahSailin | http://www.wired.co.uk/news/archive/2012-03/27/cattle-dna-traced | 14:39 |
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| n_bentha | Sorry about being a dick earlier. | 15:18 |
| yashgaroth | did you run your ligated plasmid on a gel and/or get it sequenced over the insert? | 15:18 |
| n_bentha | Anyway, the kanamycin plates of the plasmid w/ gene didn't have any visible colonies for after 1 days in the incubator. After sitting on the lab bench, bacterial colonies grew! | 15:19 |
| n_bentha | But I doubt those colonies have the right plasmid in them. | 15:20 |
| kanzure | n_bentha: it's okay i am a bigger asshole than you | 15:20 |
| n_bentha | ^^ | 15:20 |
| yashgaroth | wait whaddya mean sitting on the lab bench | 15:20 |
| n_bentha | took plates out after 1 day in the incubator | 15:20 |
| n_bentha | left it on the lab bench overnight (still covered of course). | 15:21 |
| n_bentha | colonies the next day. | 15:21 |
| n_bentha | (the plate was sitting on the lab bench, not me) | 15:21 |
| yashgaroth | one would hope | 15:21 |
| yashgaroth | so uh take me through the cloning you did | 15:22 |
| yashgaroth | double digest, gel purify, ligation, gel purify again? | 15:22 |
| n_bentha | Yup, pretty much. | 15:23 |
| yashgaroth | well, any colonies you get should have the correct plasmid, no? | 15:23 |
| n_bentha | I didn't make the plasmid...but I'm not 100% sure on that last purification step. | 15:23 |
| n_bentha | Yes they 'should' but why did one plate w/ the original plasmid have lots of colonies after day 1 in the incubator | 15:24 |
| n_bentha | But the one w/ the gene insertion didn't have any until day 2? | 15:24 |
| n_bentha | Also, there were some satelite colonies on the plate w/ original plasmid on day 2. | 15:24 |
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| n_bentha | I guess I'll have to go make the plasmid myself. Can't rely on anyone these days. | 15:24 |
| yashgaroth | if your gene insert has some background expression it could slow their growth, depends how toxic it is | 15:25 |
| n_bentha | That's what I thought! | 15:26 |
| fenn | kanzure: anything specific you want to know from DNA 2.0? | 15:26 |
| yashgaroth | doesn't bode well for the cells when you induce the promoter though | 15:27 |
| kanzure | how muh money they are making | 15:27 |
| n_bentha | But I thought the gene wouldn't have an effect in bacterial cells... | 15:27 |
| kanzure | market size | 15:27 |
| kanzure | their production costs | 15:27 |
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| kanzure | a list of all of their customers | 15:27 |
| kanzure | their primary products | 15:27 |
| n_bentha | We did make a new extract of the gene from a different plant...maybe that's it | 15:27 |
| kanzure | their roadmap/plans. | 15:27 |
| yashgaroth | they won't divulge their customer list | 15:28 |
| kanzure | they won't divulge the other info either :) | 15:28 |
| n_bentha | yashgaroth...it's a chemical inducible promoter though...maybe something from creating the plasmid is activating the promoter? that might kill the cells? | 15:31 |
| yashgaroth | possible, but if the protein is toxic then you have bigger problems | 15:32 |
| kanzure | fenn: what's up? | 15:32 |
| n_bentha | yeah. the transcribed protein destroys other proteins | 15:35 |
| n_bentha | :( No I don't think that's it yashgaroth. The previous plasmids have had the same gene in them w/ a 35s promoter, so the bacteria should have been able to recognize it. | 15:40 |
| yashgaroth | you're sure the previous ones successfully expressed the protein? | 15:42 |
| n_bentha | Yes, we verified it w/ blots. | 15:43 |
| yashgaroth | well I'd send it off for sequencing, get a read over the insertion site and see if the gene's there | 15:45 |
| kanzure | how is all of this not more expensive than just making the plasmid already? :/ | 15:45 |
| yashgaroth | sequencing costs like $10 | 15:46 |
| yashgaroth | also he has slave labor | 15:46 |
| n_bentha | Ah, the good old days of the cotton-picking south. So many coolies to do the tedious steps for me. | 15:48 |
| n_bentha | (i'm not racist, just making an observation of the current situation at the university i'm at) | 15:48 |
| yashgaroth | it's actually better than slave labor, since you don't need to pay for food and housing | 15:49 |
| n_bentha | In Capitalist America, slave pays you! | 15:50 |
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| n_bentha | http://www.bbc.co.uk/news/science-environment-17539319 | 16:50 |
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| Steel3 | Yar har. | 17:00 |
| delinquentme | interviews interviews | 17:04 |
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| fenn | off to sunny sunnyvale | 17:13 |
| kanzure | seeya | 17:14 |
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| Vicarious | hi | 17:27 |
| Steel3 | how goes, vicarious? | 17:31 |
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| delinquentme | Société Mathématique de France kanzure | 18:24 |
| delinquentme | that screams "SANITIZE ME" | 18:24 |
| Mariu | xD | 18:24 |
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| kanzure | hi wudles | 18:40 |
| wudles | Hi, just logging in to work... ;) | 18:41 |
| kanzure | wudles: what is planetx.com? | 18:41 |
| thesnark | NIBIRU | 18:42 |
| kanzure | hi thesnark | 18:42 |
| wudles | scifi / transhuman wiki ... homo excelsior. | 18:42 |
| thesnark | hey there | 18:42 |
| kanzure | wudles: okay. we do work on a transhumanist technology roadmap, including cheap lab equipment and biohacking and other practical things | 18:43 |
| kanzure | deep-fried-art: sup | 18:43 |
| n_bentha | sweet, Knights of Sidonia got an update. thanks to whoever posted the link for that | 18:44 |
| Steel3 | It's a great story | 18:45 |
| Steel3 | I love nihei's work | 18:45 |
| n_bentha | but omg it switched to left to right now | 18:45 |
| n_bentha | wait nevermind... | 18:47 |
| strangewarp | I keep misreading "futurists" as "fursuits | 18:48 |
| strangewarp | damn you, internet | 18:48 |
| Steel3 | welp | 18:48 |
| Steel3 | lol | 18:48 |
| n_bentha | LOL | 18:48 |
| Steel3 | strangewarp, where are you located out of? | 18:49 |
| strangewarp | Steel3: Boulder, CO. Currently in a bit of a rut in my life. Kind of a bullshit town if you're not monied. | 18:49 |
| Steel3 | ah | 18:49 |
| Steel3 | how far is boulder from fort collins? | 18:50 |
| strangewarp | Hmmm | 18:50 |
| strangewarp | Over to I-25, and then north for a while... I'm not really sure, haven't had any reason to drive there | 18:51 |
| strangewarp | I'd say 30 minuets to an hour | 18:51 |
| Steel3 | ah | 18:51 |
| Steel3 | I have a friend down there | 18:51 |
| strangewarp | oh nice. Fort Collins is where CSU is located, so it has a decent party scene (I am told) and it's launched a couple decent bands, more than you'd expect out of the city's population | 18:52 |
| Steel3 | yeah, my friend is working on particle accelerator design | 18:53 |
| Steel3 | at csu | 18:53 |
| strangewarp | oh rad | 18:53 |
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| deep-fried-art | kanzure: hey | 19:05 |
| kanzure | get my email? | 19:06 |
| deep-fried-art | yep, just replied | 19:07 |
| kanzure | ah okay | 19:09 |
| kanzure | yeah you had a whole task force mobilizing against you. | 19:09 |
| Steel3 | wtf happened | 19:09 |
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| deep-fried-art | yea... I do understand | 19:11 |
| deep-fried-art | also, the notion of a task force sounds pretty scary | 19:11 |
| kanzure | http://web.archive.org/web/20080708235522/http://www.fbi.gov/hq/nsb/wmd/images/hrtppe.jpg | 19:11 |
| deep-fried-art | but not as scary as that picture lol | 19:13 |
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| fenn | dna2.0 website says "tens of thousands of genes synthesized" assuming 1.5kb average that's $0.80/bp*1.5kbp*20000 = $24million in revenue | 19:21 |
| kanzure | per day? | 19:21 |
| fenn | total | 19:21 |
| kanzure | how long have they been around? three years now? | 19:22 |
| fenn | i guess they're not a public company | 19:22 |
| fenn | right | 19:22 |
| fenn | since 2003 | 19:22 |
| kanzure | so about 2500 genes per year | 19:23 |
| kanzure | that's depressing. | 19:24 |
| fenn | " Rest assured that all your genes are made in sunny California, 100% accurate and intellectual property compliant." | 19:29 |
| kanzure | intellectual property compliant! oh goodie. | 19:29 |
| fenn | there's actually a lot of information on their website | 19:29 |
| fenn | heavily paraphrased transcript http://fennetic.net/irc/2011-03-28_dna2.0_biocurious | 19:31 |
| kanzure | hoooray | 19:33 |
| kanzure | wtf 15 day turn around? | 19:34 |
| kanzure | 2 kb in 10 days? | 19:34 |
| kanzure | meh "we use non-template PCR (overlapping oligos) with some trade secret optimizations" | 19:35 |
| fenn | their rush is 5 days, apparently everything takes a couple days and they want to have a buffer for errors and re-doing the process | 19:35 |
| kanzure | how do they explain IDT having <5 days | 19:36 |
| fenn | smaller gene products i guess | 19:36 |
| fenn | "we differentiate on the science" presumably idt doesn't have as good optimization algos | 19:36 |
| kanzure | deep-fried-art: just don't do anything illegal and you'll be fine | 19:37 |
| kanzure | it's standard really.. | 19:37 |
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| deep-fried-art | I understand... I forgot for a moment that, on one level, it's serious business | 19:41 |
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| deep-fried-art | fenn: thanks for that transcript. I was hoping I wouldn't have to sift through that whole website | 19:44 |
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| nmz787 | yo | 19:50 |
| kanzure | hey nmz787 | 19:50 |
| kanzure | fenn: ping? | 19:50 |
| kanzure | we're trying to figure out wtf w/ laser cutters versus soft lithography | 19:50 |
| fenn | pong | 19:50 |
| nmz787 | ding | 19:51 |
| fenn | soft lithography = stamping a mask? | 19:51 |
| kanzure | wowowow halcyon is liquidating | 19:51 |
| kanzure | BUY EVERYTHING | 19:51 |
| nmz787 | more like making a mold, then laying elastomer on top | 19:51 |
| nmz787 | then peel off when rubbery | 19:51 |
| fenn | eh? | 19:51 |
| nmz787 | ? | 19:53 |
| yashgaroth | oh shit you weren't kidding, did musk stop giving them money? | 19:53 |
| kanzure | musk didn't give them the latest round of funding | 19:53 |
| nmz787 | i'm not finding anything on it on google news | 19:54 |
| kanzure | nmz787: i think you need to explain the context | 19:54 |
| kanzure | for fenn | 19:54 |
| nmz787 | oh | 19:54 |
| kanzure | yeah, the news takes a few hours to react | 19:54 |
| kanzure | if we hurry, we can get the equipment | 19:54 |
| yashgaroth | did they have any centrifuges | 19:54 |
| kanzure | they had all kinds of things. yes | 19:54 |
| nmz787 | link to anything? | 19:54 |
| kanzure | full machine shop. full biology lab. full chem lab. | 19:55 |
| kanzure | anselm's partner was raiding halcyon today, getting some liquid handlers | 19:55 |
| nmz787 | fenn: basically we need a way to make microstructures at least cost | 19:55 |
| n_bentha | 0_o | 19:55 |
| nmz787 | fenn: one method that looks good for prototyping microfluidics is cut-through then transfer methd | 19:56 |
| nmz787 | PDMS is layed onto acrylic, then cut through with a laser cutter | 19:56 |
| nmz787 | with enough power that the beam also chews up some acrylic | 19:56 |
| fenn | "eh?" was about halcyon | 19:56 |
| nmz787 | ensuring the PDMS isn't curved at the bottom | 19:56 |
| nmz787 | then the PDMS is bonded with an uncut sheet and peeled off the acrylic | 19:57 |
| nmz787 | on the cheap end of laser cutters we have chinese models on ebay for $800 | 19:57 |
| nmz787 | they dont have a small spot size | 19:57 |
| nmz787 | which is accomplished by first expanding the beam size, then focusing it again | 19:58 |
| fenn | for such a small spot i'd imagine a low power diode would do fine | 19:58 |
| nmz787 | (wider beam can be focused more tightly) | 19:58 |
| nmz787 | (more easily) | 19:58 |
| fenn | any reason we need a high power (>25W) laser? | 19:58 |
| nmz787 | nah | 19:58 |
| nmz787 | well diode beams aren't as nice as CO2 | 19:59 |
| nmz787 | or rather non-diode lasers | 19:59 |
| fenn | because they're not circular? | 19:59 |
| nmz787 | because the diodes tend to be less coherent, and yeah not circular | 19:59 |
| fenn | elliptical gaussian because of side-exit | 19:59 |
| fenn | that can be corrected btw | 19:59 |
| nmz787 | or adding multiple diodes into one light pipe | 19:59 |
| nmz787 | get weird shapes | 20:00 |
| fenn | i like diodes because they're small and lightweight thus you don't need fancy optics | 20:00 |
| nmz787 | but anyways CO2 is better for acrylic | 20:00 |
| nmz787 | as you said to correct the beam, you need more optics than with a non-diode laser | 20:00 |
| fenn | so, what's the point of trying to do it all in one step, instead of etching in a solution? | 20:00 |
| nmz787 | how do you control where you etch? | 20:01 |
| fenn | you mask off parts of the glass | 20:01 |
| nmz787 | what glass? | 20:01 |
| fenn | photo polymerizable resin | 20:01 |
| fenn | huh? | 20:01 |
| nmz787 | right that's the other option | 20:01 |
| nmz787 | soft-lithography | 20:01 |
| kanzure | "hacker dojo is fucked. they got a fire code violation. gotta spend 250k to upgrade fire systems" | 20:01 |
| fenn | i mean glass instead of acrylic | 20:01 |
| nmz787 | which we could either send out for | 20:01 |
| nmz787 | or use LCD | 20:02 |
| fenn | kanzure: it's overblown, mtn view is just trying to extract money from them | 20:02 |
| nmz787 | toner on transparency sucks | 20:02 |
| fenn | no, use the laser to polymerize a mask onto glass directly | 20:02 |
| fenn | like is done for PCB etching | 20:02 |
| nmz787 | most resins are in the UV | 20:02 |
| * fenn shrugs | 20:02 | |
| nmz787 | excimer lasers are really expensive | 20:02 |
| n_bentha | 250k?!?! | 20:03 |
| nmz787 | maybe there are better/other resins | 20:03 |
| fenn | i believe there are UV diode lasers | 20:03 |
| fenn | anyway there are blue light curing resins and other more fancy stuff | 20:03 |
| fenn | the reason PCB's are traditionally green is they use an IR cure epoxy for solder mask | 20:03 |
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| fenn | so, basically i've heard that pdms sucks because it's too poroous | 20:04 |
| fenn | and i'm trying to figure out how to do this without pdms | 20:04 |
| kanzure | i don't think you can do pressure valves with glass tho | 20:04 |
| nmz787 | nope | 20:05 |
| nmz787 | PDMS is great for some things | 20:05 |
| nmz787 | other things porosity becomes an issue | 20:05 |
| nmz787 | or tricky | 20:05 |
| fenn | ok so what's the minimum resolution needed to start with? | 20:06 |
| nmz787 | i was thinking 25 micron channels | 20:06 |
| kanzure | it would be nice to have 1 micron control but w/e | 20:06 |
| nmz787 | http://www.kellerstudio.de/repairfaq/sam/laserioi.htm#ioicdf | 20:06 |
| nmz787 | yeah | 20:06 |
| nmz787 | well channel width isn't directly the same as beam control | 20:07 |
| kanzure | yeah it depends on whether we're doing cut-through channels or just etching with the beam into the material to make some depth | 20:07 |
| nmz787 | 1000 dpi gets you 25.4 microns / step of a motor | 20:07 |
| fenn | cant we just use a microscope and shoot the laser through the eyepiece? | 20:08 |
| nmz787 | possibly | 20:08 |
| nmz787 | i guess depends on the glass | 20:08 |
| nmz787 | if its blue, prob | 20:08 |
| fenn | yeah glass is UV absorbent | 20:08 |
| nmz787 | blue light | 20:08 |
| fenn | i've forgotten everything i knew about lasers | 20:09 |
| nmz787 | 3 axis CNC setup basically is needed | 20:09 |
| fenn | an off the shelf CNC won't get you 1 micron | 20:09 |
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| kanzure | i was just bullshitting with 1 micron, we can probably get away with something bigger | 20:09 |
| fenn | 50 micron is typical, 10 if it's super fancy | 20:09 |
| kanzure | but it would be nice to have smooth curves at some resolution | 20:09 |
| fenn | yes | 20:10 |
| nmz787 | using 1/4 40 screws, one turn moves 15.87 microns | 20:10 |
| nmz787 | motors can be microstepped to 256 places | 20:10 |
| fenn | pixelated channels seems wonky | 20:10 |
| nmz787 | atoms are picels | 20:10 |
| nmz787 | pixels | 20:10 |
| fenn | yes differential threading can do arbitrary step/movement ratio | 20:10 |
| fenn | basically one thread goes forward the other goes backwards, the difference is the travel | 20:11 |
| nmz787 | 1/4 40 screws are easy to come by | 20:11 |
| nmz787 | and we can add a simple interferometer using a photodiode to feedback to the controller if better precision is needed | 20:11 |
| fenn | actually i might be wrong about the repeatability of typical CNC's | 20:12 |
| kanzure | i doubt 50 micron is typical for cnc? | 20:12 |
| fenn | usually they're specified in terms of accuracy over the entire bed | 20:12 |
| nmz787 | this is basically what i just described http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CE8QFjAB&url=http%3A%2F%2Fwww.himt.de%2Fen%2Fproducts%2Fdwl66fs.php&ei=I9FzT-uXEoTk0QHvw93_Ag&usg=AFQjCNEsU4of4ZQEy9cz5UxegCAtK_V9dw&sig2=TSeSKWc_XXVq_aE1fSd64w | 20:13 |
| nmz787 | err | 20:13 |
| fenn | i presume we don't really care about accuracy as long as it's repeatable error | 20:13 |
| nmz787 | http://www.himt.de/en/products/dwl66fs.php | 20:13 |
| nmz787 | they have a 6 month lead time or something | 20:13 |
| nmz787 | and i think they want around $250k | 20:13 |
| fenn | that looks like overkill | 20:13 |
| nmz787 | for something that could almost be done using old CDROM drives | 20:14 |
| fenn | um | 20:14 |
| fenn | the reason cd-rom works is it uses closed-loop analog(?) feedback from the track reflection | 20:15 |
| fenn | using dvd diode is an interesting idea though | 20:15 |
| n_bentha | 250k! You could upgrade your fire-system for that! | 20:15 |
| fenn | er blu-ray, whatever is higher energy | 20:16 |
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| fenn | cd-rom is 787nm, dvd is 657nm, blu-ray is 405nm | 20:17 |
| nmz787 | no i meant cdrom for the gantry and rubber bushings | 20:17 |
| nmz787 | http://www.yamahamultimedia.com/yec/tech/discta2_01.asp | 20:17 |
| nmz787 | right cd/dvds use analog feedback via the spiral, but thats why i added in the interferometer | 20:18 |
| fenn | i'm wary of interferometry | 20:18 |
| nmz787 | lol | 20:18 |
| nmz787 | why? | 20:18 |
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| nmz787 | http://www.metacafe.com/watch/1381543/laser_interferometer_homemade_for_20/ | 20:19 |
| fenn | they're generally a pain in the ass | 20:19 |
| nmz787 | put a photodiode at the image in this setup | 20:19 |
| nmz787 | and you get a sine wave out | 20:19 |
| fenn | bleh i can't see that video | 20:19 |
| nmz787 | add a comparator and you have digital ticks out | 20:19 |
| nmz787 | the worst part is vibration from the room or the system (motors) | 20:21 |
| nmz787 | or rather what you have to watch out for | 20:21 |
| * fenn eyes the 8:40 caltrain | 20:22 | |
| nmz787 | unless i find something better | 20:23 |
| nmz787 | looks like i'll be diving into this | 20:23 |
| nmz787 | http://www.maxreason.com/software/optics/opus.html#overview | 20:23 |
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| fenn | ok gotta go or i'll be puttering here for another hour | 20:25 |
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| kanzure | aw don't disconnect | 20:29 |
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