| --- Log opened Mon Feb 20 00:00:18 2012 | ||
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| chris_99 | anyone done IR spectography before? | 03:31 |
|---|---|---|
| chris_99 | *spectroscopy | 03:32 |
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| utopiah | what's your favorite QuantifiedSelf Show&Tell video? (including the ones done by people in this chatroom) | 03:44 |
| Steel2 | I don't even know what the hell that is | 03:47 |
| utopiah | presentation for http://quantifiedself.com | 03:48 |
| utopiah | during meetings people come and show what they have done (rather than discuss theory) | 03:49 |
| utopiah | or advertize products | 03:49 |
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| kanzure | `At least a University with a backbone! Others for example in Canada let publishers sift through the private emails of their faculty members so they can spot copyright violations ( http://www.cautbulletin.ca/).` | 06:47 |
| nsh_ | first against the wall, &c. | 06:48 |
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| * ybit digs around and tosses three trouts into the center of the room | 12:00 | |
| yottabit | fenn: what have you been working on lately | 12:05 |
| yottabit | kanzure: did you finish the pr disassembly? | 12:07 |
| yottabit | fenn: i'm a bit confused by your log, not enough info to properly stalk without talking with you directly which defeats the entire concept | 12:08 |
| yottabit | ..of stalking | 12:09 |
| kanzure | yottabit: the pokered disassembly is going fine | 12:10 |
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| kanzure | yottabit: http://bitbucket.org/kanzure/pokered/changesets | 12:10 |
| kanzure | there's still a few hundred thousand bytes left | 12:11 |
| kanzure | bank $7 has a lot of music and is completely undissasembled | 12:11 |
| kanzure | i disassembled most of the textbanks though, i don't think there's much left on that front | 12:11 |
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| ParahSailin__ | does anyone know what sort of royalty stream breakoutlabs expects? | 12:30 |
| kanzure | stream? well they put numbers on their site | 12:31 |
| kanzure | https://www.breakoutlabs.org/faqs.html | 12:31 |
| ParahSailin__ | right im there, i just dont see numbers | 12:31 |
| kanzure | oh they removed it? | 12:31 |
| kanzure | "We have two forms of funding agreements: a research grant, in which the researcher commits a royalty stream and company warrants back to Breakout Labs in the event of successful commercialization and an IP agreement, in which Breakout Labs retains IP and commits a royalty stream back to the applicant in the event of successful commercialization." | 12:32 |
| kanzure | it used to be more specific.. let me see if i have a backup | 12:33 |
| kanzure | welp. no i don't. | 12:36 |
| kanzure | wait, neither of those are the traditional funding models | 12:38 |
| kanzure | the second one is extremely aggressive | 12:38 |
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| _sol_ | I got a crazy one... just as a joke I guess.. DIY comparative anatomy and bio... | 14:45 |
| _sol_ | not just on game or farm animals... | 14:45 |
| _sol_ | I guess ya might piss off some PETA ppl in the least and maybe step on vet laws at most | 14:45 |
| _sol_ | although 100 yrs ago, most DIY was clear and in the open... | 14:46 |
| _sol_ | I guess ya could do it on hunting season though.. just preservation... | 14:46 |
| _sol_ | the problem is if I want to do primates and humans I'll need to find some volunteers and a storage locker... :P I guess the local DIY butcher bio-amatuer sci is ou tof hte question for private contracted biosciences unless the libertarians take over and the extreme libetarians tear down the FDA and a few other agencies along with state regs on medical practice ... j/king | 14:47 |
| _sol_ | 1850s live theatrical anatomy and vivisectioning of larger animals with vivication via electrical stimulation... I guess those DIYers won't be able to do tha tagain 'xept on small animals... | 14:48 |
| Mokbortolan_ | just go to Germany, I'm sure you can find someone with a fetish for being dissected | 14:48 |
| Mokbortolan_ | Craigslist FTW! | 14:49 |
| _sol_ | heh... I did have htis weird thought before about what the world would look like with some libetarian in US who tear down the medical laws, ya might get some breakthroughs faster but alot of private contracts will jamlog the courts over the ppl who they fail to deliver the breakthroughs on | 14:49 |
| _sol_ | contracts would be jamming the courts... | 14:50 |
| _sol_ | H+ might come alot faster | 14:50 |
| _sol_ | but at the expense of crooked contracts with lawyers and doctors seeking test subjects I think | 14:50 |
| _sol_ | and ya'd have pottown on one side of the tracks and deadheadville farther out with the harddrug party scene that is heavily taxed run by some screwy cops and some lords of the drugs... be it some weird legit world... | 14:52 |
| _sol_ | anyway, just bad ideas I think for alot of sutff whcih is why I'm not a pure libertarian transhumanist | 14:52 |
| uniqanomaly_ | _sol_: just make few billions and fund all the research no matter how unethical in some bunker in africa | 14:53 |
| _sol_ | ya prob... | 14:53 |
| _sol_ | I could start the cross breeding program | 14:53 |
| _sol_ | and pay some indian mothers to incubate the embryo to term | 14:53 |
| uniqanomaly_ | nah | 14:53 |
| _sol_ | until I get some bioreactor biomed research finished | 14:53 |
| _sol_ | heh | 14:53 |
| uniqanomaly_ | all you need is Nikola Tesla's DNA | 14:53 |
| _sol_ | er likew a artificial womb | 14:53 |
| uniqanomaly_ | like 100 clones | 14:54 |
| uniqanomaly_ | you get singularity in 15 years | 14:54 |
| _sol_ | I'm pragmatic. I think social inertia will delay alot of this stuff | 14:54 |
| _sol_ | the basic transhumanism that is... | 14:54 |
| _sol_ | not talking the fantastic and far out | 14:54 |
| uniqanomaly_ | and thats why you just can't rely on it | 14:54 |
| _sol_ | social inertia and govt regs | 14:54 |
| _sol_ | I mean the lobbiest could form a brick wall against some research that ya'd have to really create a spectacle to tear down | 14:55 |
| _sol_ | conservative and religious lobby | 14:55 |
| _sol_ | I think gene therapy is still off limits after some kid died at john hopkins decade or more back | 14:55 |
| uniqanomaly_ | hmm heres an idea | 14:56 |
| _sol_ | but I don't recall the details of that study except they cross contaminated the engineered virus with some flu bug or something by accident and he died of an infection | 14:56 |
| uniqanomaly_ | H+ people learning acting at hollywood level and skilling human interaction and brainwashing | 14:56 |
| uniqanomaly_ | like few hundred of them | 14:56 |
| _sol_ | a few movies might help | 14:56 |
| _sol_ | I thought of that. | 14:56 |
| uniqanomaly_ | and taking over all poliics | 14:56 |
| _sol_ | There hasn't been really any H+ movies. | 14:56 |
| uniqanomaly_ | screv movies, I mean acting and brainwashing for voters | 14:57 |
| _sol_ | We need a speilberg with poliitcal and scientology connections. I heard a bunch of wealthy actors believe in scientology so heh... | 14:57 |
| _sol_ | if ya want those powers scientology promised... star in these films | 14:57 |
| _sol_ | :P | 14:57 |
| _sol_ | or not | 14:58 |
| _sol_ | well, I htink movies bring in abit of revenue and search as PR for tech in some sense | 14:58 |
| _sol_ | not that many watch documentaries as movies | 14:58 |
| _sol_ | er I mean search=serve as | 14:58 |
| _sol_ | I think kurzweil was suppose to create some fictional movie, but it turned into a documentary I think | 14:59 |
| uniqanomaly_ | I was talking about hollywood-level acting, brainwashing, human interaction with application in politics | 14:59 |
| _sol_ | oh... | 14:59 |
| _sol_ | public spin games? | 14:59 |
| uniqanomaly_ | few hundred of h+ people with hidden agenda play they way through to highest levels of power | 15:00 |
| _sol_ | I mean someone who can twist the public by charm and appeal to a particular agenda without letting everyone in on it. | 15:00 |
| _sol_ | It's already in the republican party. It's called Supersoldier something of 2020 or some odd date that I recall reading about. They have these ideas from battle suits to bioengineering for soldiers. They also have the huge influx of robotic money coming from DARPA. | 15:01 |
| kanzure | yeah, recovering nikola tesla's dna is on my todo list | 15:01 |
| kanzure | there's a lot of graves i'd like to dig up for dna | 15:01 |
| _sol_ | and the democrats have stem cells and somehow the middle ground conservatives want to swing either side to mix pro-life and biotech into one big anti-agenda | 15:02 |
| _sol_ | so ... | 15:02 |
| _sol_ | hmm | 15:02 |
| _sol_ | ,er and=but somehow the middle... | 15:02 |
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| _sol_ | I guess they fear biotech firms buying out the bio tissues from abortion clinics which from a business standpoint I would see someone somewhere trying to cash in to use it as some sort of feedstock for the early developmental cells and stem cells and stuff, but ya know ya'd get such a huge reaction out o fthat business proposal in politics I mean...forget it... | 15:04 |
| kanzure | who's doing the fearing? what? | 15:05 |
| _sol_ | its like start with embryos, open it up to 1st term, and then ya'd have a whole experimental industry... well, the religious conservative probably have some nightmere scenarios in there head | 15:05 |
| _sol_ | but then if the mothe rsigns off her biotissue as hers and to sell it for whatever.. then | 15:05 |
| _sol_ | bu tthen that opens a can of political worms | 15:05 |
| _sol_ | er their heads | 15:05 |
| _sol_ | I've just debated this with some philosophy people before playing the devil's advocate so I've seen some reactions... | 15:06 |
| _sol_ | some ppl are very opinionated and/or belief hardened to one view | 15:06 |
| _sol_ | I mean they already carve up people into body bags for experimental and transplant research/donation from donors in accidents and at death.... | 15:07 |
| _sol_ | I remember watching this company that collects musculoskeletal tissue from donors to turn into I guess tissue parts for orthopedic research and replacements | 15:08 |
| _sol_ | I guess extra tendons, cartilage etc... they have this huge biotech factory tha tdoes that I saw on some taboo show on national geographic before... | 15:08 |
| _sol_ | it was like bodybag city | 15:08 |
| _sol_ | they use everything | 15:08 |
| _sol_ | after they take the major orgons out | 15:09 |
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| _sol_ | anyway | 15:09 |
| kanzure | someone should make a scholar.google.com interface that extracts graphs/charts/tables based on your query | 15:19 |
| kanzure | bleh that someone is going to have to be me isn't it | 15:26 |
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| Juul | kanzure, always | 15:27 |
| Juul | you still working on skdb kanzure? | 15:28 |
| Juul | hm, last update two years ago? | 15:29 |
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| kanzure | Juul: the most recent skdb-related work i've done is the commits in the lolcad repository | 15:31 |
| kanzure | because i figured i needed better cad | 15:31 |
| Juul | ok | 15:31 |
| kanzure | cad is sorta tricky heh | 15:32 |
| Juul | i believe you | 15:32 |
| Juul | what's your main project nowadays? | 15:33 |
| kanzure | right now i'm working on a microfluidic dna synthesizer | 15:33 |
| Juul | :) | 15:34 |
| kanzure | Juul: do you have a post-lbl plan? | 15:35 |
| Juul | kanzure, i have a few ideas. i'm meeting with drew endy tomorrow and i'll see what he has to offer. | 15:36 |
| kanzure | hrmm that's not quite what i imagined when you said you wanted to live as a scruffy freedom hacker for a while | 15:37 |
| kanzure | :P | 15:37 |
| kanzure | iirc drew is still being drew at his stanford lab? | 15:37 |
| Juul | hehe, yeah he is. yeah i'm not really keen on staying with the BIOFAB post shutdown/transformation, but i want to talk to drew before making any decisions. | 15:37 |
| kanzure | makes sense | 15:38 |
| Juul | i do need a visa, so maybe i can have something part time | 15:38 |
| Juul | but otherwise i'm working on a decentralized trust-group-based file-sharing platform | 15:38 |
| Juul | kinda like dropbox but peer to peer | 15:38 |
| Juul | and usable without an internet connection | 15:38 |
| kanzure | thesnark (in here) keeps claiming he's been working on a better-than-freenet p2p caching thing for paper sharing | 15:39 |
| kanzure | but i haven't seen any code yet | 15:39 |
| Juul | ok | 15:39 |
| Juul | that sounds like a complex project | 15:39 |
| Juul | freenet is not simple | 15:39 |
| kanzure | yeah, a syncable sneakernet thing would be nice | 15:39 |
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| kanzure | hi yashgaroth | 15:40 |
| yashgaroth | 'lo | 15:40 |
| Juul | mm, first version will have zeroconf support for just connecting a bunch of computers on a LAN / ad-hock wifi | 15:40 |
| Juul | but eventually i'll want to integrate wifi meshing, sneakernet sync, bluetooth, etc. | 15:40 |
| kanzure | so people keep telling me that mail order dna synthesis is better than having a device | 15:40 |
| kanzure | but this just boggles my mind.. first, synthesis prices over the web are outrageous and impractical for doing really interesting things | 15:41 |
| Juul | bah, i'm sure they said that about mainframes vs. personal computers | 15:41 |
| kanzure | well $0.20/bp is like saying you're okay with $0.20/transistor on your chip.. yeah right | 15:41 |
| Juul | mmm | 15:41 |
| kanzure | and even considering that, oligo prices are supposedly 'falling' (or so rob claims) | 15:41 |
| kanzure | but what's their business model when it falls to $0.0001/bp | 15:41 |
| Juul | eventually we'll have in-vivo dna synthesis, where you just grow a culture while controlling enzyme operation with e.g. flickering LEDs | 15:42 |
| kanzure | yeah of course | 15:42 |
| kanzure | but nobody has invented that yet ;) | 15:42 |
| Juul | yeah it's gonna take a while | 15:42 |
| kanzure | right now i am interested in a very simple chemical oligo synthesizer (for 20-30 bp max) | 15:42 |
| yottabit | i never saw this two years ago: http://www.youtube.com/watch?v=_piO849uRdI :: autonomous sliding parallel parking | 15:42 |
| kanzure | and an oligo library device | 15:42 |
| Juul | i agree that desktop synthesis is the way to go. | 15:42 |
| kanzure | one of the difficulties i am having is convincing some people of that | 15:43 |
| kanzure | even andrew hessel says he prefers mail order synthesis | 15:43 |
| kanzure | which boggles my mind. | 15:43 |
| Juul | well it's likely because they don't realize how reliable and cheap desktop synthesis can get | 15:43 |
| kanzure | joseph jackson too. | 15:43 |
| Juul | and how a centralized business model will not be able to compete at all | 15:43 |
| Juul | for now it makes sense to use mail order synthesis | 15:44 |
| kanzure | well i would think our own cells are good examples of super cheap synthesis | 15:44 |
| Juul | but very soon it won't | 15:44 |
| Juul | exactly | 15:44 |
| kanzure | $5/day in food = 100 billion cells making dna each day | 15:44 |
| Juul | we "just" need to be able to control the synthesis with outside input instead of having it based on templates | 15:44 |
| Juul | i've been thinking about how to accomplish that | 15:45 |
| kanzure | everyone has. | 15:45 |
| kanzure | absolutely everyone. | 15:45 |
| kanzure | i think we should organize those people somehow he | 15:45 |
| kanzure | *heh | 15:45 |
| Juul | well, everyone with any form of vision | 15:45 |
| kanzure | ParahSailin__ recently joined this chan | 15:45 |
| kanzure | and he's had the same thoughts, which was nice to find | 15:45 |
| kanzure | but fenn, you, i think yashgaroth said it too, cathal, nathan, andrew.. | 15:45 |
| kanzure | if you want my notes on the topic, see http://diyhpl.us/~bryan/papers2/polymerase/ | 15:46 |
| yashgaroth | I'm still a bit more cautious than everyone else you mentioned, but yes you can include me on the list | 15:46 |
| kanzure | i think it would be useful to get those people collaborating somehow | 15:46 |
| kanzure | it's tempting to think that you're going to 'crack the code' on your own, but that probably won't happen | 15:47 |
| Juul | ok i'll have a look at your notes | 15:47 |
| kanzure | well anyway-- | 15:47 |
| Juul | yeah collaboration is the way to go | 15:47 |
| kanzure | i'd also appreciate advice on how to convince people against mail order synthesis | 15:47 |
| kanzure | i need some sort of structural argument if i'm going to be pitching to investors soon | 15:47 |
| Juul | which is one of the reasons i'll likely be working to create better tools for small heterarchical groups | 15:48 |
| kanzure | i have a few meetings lined up, and this particular question has been killing me in some conversations | 15:48 |
| kanzure | heh it's also a little awkward.. old school vc is for high risk, high reward ventures | 15:49 |
| kanzure | but dna synthesis is surprisingly low risk | 15:49 |
| kanzure | /services/ are low reward | 15:49 |
| Juul | hm, i'd compare it to other industries. pick a few that have moved from centralized to desktop, some that have partially moved, and some that haven't. then show what caused the move to desktop to happen in those cases, and why it's still preferable to have centralized business models in others. identify the factors that make the difference between "centralized long-term sustainable" vs the opposite | 15:49 |
| Juul | then apply that to the case of DNA synthesis | 15:49 |
| kanzure | printers? heh | 15:50 |
| Juul | printers have partially moved | 15:50 |
| Juul | computing has completely moved | 15:50 |
| Juul | eletronics components have not really moved at all | 15:50 |
| Juul | though an argument can be made for FPGAs being a bit of a move | 15:50 |
| yashgaroth | just find some ex-SV vc people and tell them it'll be like when we went from mainframes to desktops, they'll love it | 15:50 |
| kanzure | yashgaroth: haha, i've always been confused by everyone using the 'homebrew computer club' as a comparison to diybio | 15:51 |
| kanzure | people love that analogy, but i don't know if it works | 15:51 |
| yashgaroth | you don't need the whole metaphor, just the sense of "a computer in every house" | 15:51 |
| kanzure | and the people who love that analogy are usually not the people who would have been members of the homebrew computer club anyway | 15:51 |
| Juul | kanzure, it will work if you, in a DIYBIO setting, make affordable effective microfluidics available to everyone :) | 15:52 |
| kanzure | Juul: sure.. i have no doubt that it will work out | 15:52 |
| kanzure | but i need to relay this to other people if i want more funding than my own | 15:52 |
| Juul | i meant the metaphor will work out | 15:52 |
| kanzure | oh. hrm. | 15:53 |
| Juul | i'm sure you're sure of your own project, or you wouldn't be doing it :) | 15:53 |
| yashgaroth | you don't necessarily need to push the desktop aspect, just that it'd be cheaper than the current methods, which presumably it will be | 15:53 |
| kanzure | it's interesting to note that oxnano has realized this for sequencing | 15:54 |
| kanzure | i.e. a cheap device opens up the market | 15:54 |
| kanzure | *grows the market | 15:54 |
| Juul | well, the main thing that causes centralization to be less expensive in some cases is high startup and maintenance costs, where you either need a large initial investment or there are continued running costs that can only be justified if you have a high level of utilization of the equipment | 15:55 |
| kanzure | i think a good argument against mail order dna synthesis companies is that when the price drops to $0.00001/bp they will not exist anymore | 15:55 |
| yashgaroth | where did you get that figure from | 15:56 |
| kanzure | i am just making it up | 15:56 |
| kanzure | they still need to be able to pay for their employees | 15:56 |
| Juul | well, you could have very cheap synthesis which is only very cheap if you buy expensive machines and utilize them at close to 100% to offset the initial investment and baseline per-day running costs, and then centralization would still be preferred. | 15:56 |
| Juul | you need to show that this will not be true | 15:56 |
| kanzure | then there's reagents and equipment (which, let's say, is some fixed investment that we can factor out) | 15:56 |
| kanzure | right | 15:57 |
| kanzure | i've been writing a simple python script | 15:57 |
| kanzure | that calculates the operating costs of a dna synthesis service | 15:57 |
| Juul | cool | 15:57 |
| Juul | the kanzure equation | 15:57 |
| kanzure | so at minimum they have reagents, initial investment in equipment, maintenance on equipment, marketing costs, and salaries | 15:57 |
| kanzure | i think salaries are the big one for dna synthesis services | 15:57 |
| yashgaroth | really? it's mostly automated | 15:58 |
| kanzure | you still need people in the company | 15:58 |
| Juul | there is a bunch of prep work still | 15:58 |
| yashgaroth | someone to collect the money | 15:58 |
| kanzure | marketing is a bit fuzzy | 15:58 |
| kanzure | obv. competing dna synthesis services must dump money into marketing/advertising to compete with each other | 15:58 |
| kanzure | if they aren't competing on price, it's on brand.. and that has its own costs | 15:59 |
| kanzure | which, realistically, could be google adwords costs? heh | 15:59 |
| kanzure | actually i really like that. it's easy to go get some cost per click estimates | 15:59 |
| kanzure | i should probably be tracking that on google adwords. as cpc goes up over time it indicates stronger competition between oligo synthesis services | 16:00 |
| kanzure | so anyway - there's a minimum operating cost for running a dna foundry | 16:01 |
| Juul | the question is, if you can do synthesis with a low initial investment, no dedicated personnel, very little time-investment for prep/post procedures, no per-day running costs (only per-nucleotide), then what is the argument for using a centralized service? | 16:01 |
| Juul | i can think of a few | 16:01 |
| Juul | 1. it's still slightly easier | 16:01 |
| Juul | 2. it still requires a bit of training and a bit of time and a bit of money to start using the desktop device | 16:02 |
| yashgaroth | the FBI likes you better if it's centralized and recorded | 16:02 |
| Juul | 3. they may have better quality assurance | 16:02 |
| kanzure | #2 is sorta iffy.. you already need to be doing other biology lab activities in the first place. dna prep is a common operation. | 16:03 |
| Juul | 4. it's easier to comply with government regulation | 16:03 |
| Juul | kanzure, true | 16:03 |
| kanzure | #3 is definitely true for now. i'd have to include a sequencer on the chip | 16:03 |
| Juul | i think 3 and 4 are going to be the tough ones to handle | 16:03 |
| Juul | when convincing VPs | 16:04 |
| kanzure | #3 is an interesting problem for sure, but i think on-chip verification is a real possibility | 16:04 |
| Juul | yeah | 16:04 |
| Juul | if the target audience for your device is the DIYbio scientist in the U.S. then there is a chance that state laws, such as the one preventing you from using 23andme in New York, will block the sale of your device | 16:05 |
| kanzure | i think that hobbyist use is super important | 16:05 |
| kanzure | but lots of people will buy a $5k dna synthesizer | 16:06 |
| Juul | yes | 16:06 |
| Juul | so #3 is likely your main worry then | 16:06 |
| Juul | i've seen companies use a more expensive third party solution because of _perceived_ better quality assurance | 16:06 |
| Juul | sometimes it's easier to have someone outside to blame when something fails | 16:07 |
| kanzure | i'm sure companies with big budgets would prefer more quality assurance | 16:07 |
| kanzure | yeah for sure | 16:07 |
| kanzure | "Gold Certified dna synthesis" | 16:07 |
| Juul | yep | 16:07 |
| yashgaroth | if you can get >10% of your syntheses of ~1kb to be correct, that's all you need | 16:07 |
| yashgaroth | pick out 20 transformed colonies until you get a good one, and start stringing them together | 16:08 |
| kanzure | well, if i make the chemical oligo chip first, i think only 10-20bp is expectable | 16:09 |
| kanzure | the ligation chip can probably do better | 16:09 |
| kanzure | granted, this is a 6 month outlook | 16:10 |
| yashgaroth | yeah I mean the ligation step, 6mers are still pretty ideal | 16:10 |
| Juul | kanzure, do you want to start a group around in-vivo / in-vitro synthesis? we could just put up a piratepad, wiki or mailing list? | 16:11 |
| kanzure | yeah for sure | 16:12 |
| kanzure | but what are you thinking when you say in vivo? are you talking about a polymerase mechanism, or something else? | 16:12 |
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| kanzure | hi Lethena | 16:14 |
| Juul | i've only thought about using polymerases or enzymes with similar activity, existing or modified, plus possibly modified nucleotides, to accomplish this | 16:14 |
| Lethena | Oh, hi! | 16:14 |
| kanzure | Juul: i don't think a mailing list or wiki would accomplish things per-se, i think those would be useful tools to communicate | 16:14 |
| kanzure | but | 16:14 |
| kanzure | i think it should be a project to write/collaborate on a strategy doc | 16:14 |
| kanzure | for imagining methods or experiments to develop this technology | 16:15 |
| Juul | it would probably be useful to start with a brainstorm | 16:15 |
| kanzure | of course | 16:15 |
| Juul | to see what kinda ideas are out there | 16:15 |
| kanzure | the doc could also include simulations/models of the pdb data, a rational protein engineering review and an analysis of existing known polymerases (of which are there are a shitload) | 16:15 |
| Juul | we could have a long brainstorm | 16:15 |
| Juul | oh | 16:15 |
| Juul | yeah definitely | 16:16 |
| Juul | i think the first goal should be to gather as many different ideas as possible, and the second to identify one or more most likely paths to a successful first partial or complete prototype | 16:16 |
| kanzure | did you ever see the 'whole brain emulation review'? | 16:16 |
| Juul | nope :) link? | 16:17 |
| kanzure | there's lots of these types of docs i think, but i liked that one in particular | 16:17 |
| kanzure | http://diyhpl.us/~bryan/papers2/neuro/brain-emulation-roadmap-report.pdf | 16:17 |
| kanzure | sorry. *whole brain emulation roadmap | 16:17 |
| Juul | thanks! | 16:17 |
| kanzure | does this seem like a good thing to aim for | 16:18 |
| ParahSailin__ | here, reading backlog | 16:18 |
| Juul | kanzure, yeah i like it | 16:18 |
| kanzure | Juul: just to clarify, do you currently have a thorough plan that you think would work? | 16:19 |
| kanzure | 'cause everyone else i've talked with has been grasping at straws | 16:19 |
| kanzure | the most expensive dna synthesizer on ebay is only $14k.. what's up with this? | 16:21 |
| Juul | no, only half-ideas, like using the most unspecific polymerases available, then attempting to make modified nucleotides that are coupled to light-switchable proteins such that they become available only under light of a specific wavelengths, and coupling the two in-vitro to toggle availability of GATC as the polymerase progresses. even if that long-shot idea would work, you'd still need to somehow "clock" the polymerase, as the availability switching | 16:22 |
| Juul | will be less than instant and the polymerase activity is stochastic | 16:22 |
| kanzure | oh, light-switchable-proteins attached to *nucleotides* is a new one.. | 16:23 |
| Juul | yeah :) | 16:23 |
| Juul | since proteins are hard to modify | 16:23 |
| kanzure | lots of the methods talked about in here have been things like, | 16:23 |
| Juul | i suggest we attempt to find a solution that doesn't require any protein design | 16:23 |
| kanzure | "well, sprinkle in some chromophores into polymerase and pray" | 16:23 |
| Juul | hm | 16:23 |
| kanzure | yeah, avoiding protein design would be nice | 16:23 |
| kanzure | clocked polymerase would involve something like a "go ahead and polymerase / don't accept new nucleotides" and a "accept nucleotide but don't polymerize" mode that we could toggle it between | 16:24 |
| kanzure | *and polymerize | 16:24 |
| Juul | yeah | 16:24 |
| Juul | we may be able to evolve such a protein, but i haven't come up with anything solid | 16:25 |
| ParahSailin__ | i did a lot of research on light-switchable proteins | 16:25 |
| ParahSailin__ | most of the existing work, too slow, too little change in activity | 16:25 |
| kanzure | 1) electronic control of polymerase | 16:26 |
| kanzure | 2) nucleotide gun made out of a nanotube pointed at the finger domain of dna polymerase | 16:26 |
| kanzure | 3) single-polymerase water droplet & add in a single dNTP at a time | 16:26 |
| kanzure | 4) physical display of dNTP as template for current base addition (i.e., on a stick) | 16:26 |
| kanzure | 5) a protein that can undergo conformational changes that polymerase thinks represents the template strand | 16:26 |
| kanzure | 6) pull/push a template through DNA polymerase to control which dNTP it should be selecting for | 16:26 |
| ParahSailin__ | i would look at something like physically distorting a protein, using an afm tip of magnetic microparticles | 16:26 |
| kanzure | 7) protein-template DNA polymerase, where the polymerase itself has a giant protein that enzymatically encodes dNTP information | 16:26 |
| kanzure | 8) graph grammar rules of valid thumb/fingers/pad/palm domains of polymerases to generate a library of possible polymerase variants | 16:26 |
| kanzure | 9) mechanical pressure on polymerase | 16:26 |
| kanzure | 10) ultrasound | 16:26 |
| kanzure | oh could we magnetize a polymerase molecule? | 16:26 |
| kanzure | that would be fun | 16:26 |
| Juul | woah | 16:26 |
| ParahSailin__ | biotinylate a residue, used streptavidin-magnetic microsphere | 16:27 |
| kanzure | yeah but you'd have the microsphere, not the polymerase at the end of the biotin | 16:27 |
| Juul | magnetize it? there are examples of electromagnetic-switchable enzymes, but the effect is more subtle than light-switchable (not that light isn't electromagnetism, but you catch my meaning) | 16:27 |
| ParahSailin__ | afm tip *or magnetic | 16:27 |
| kanzure | i mean, the polymerase wold be free-floating on the end of the strand | 16:28 |
| ParahSailin__ | then attach the polymerase on the other side to the well | 16:28 |
| kanzure | Juul: nah, like magnetize it as a way to help get an afm tip locked on to it possibly | 16:28 |
| Juul | oh | 16:28 |
| ParahSailin__ | afm tip separate idea from magnetic particles | 16:28 |
| kanzure | oh okay. | 16:28 |
| ParahSailin__ | i got stuck on the napkin math for magnetic particles though | 16:28 |
| ParahSailin__ | i dont know what a reasonable switching rate or force would be | 16:29 |
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| kanzure | well there's also weird ideas like- | 16:29 |
| kanzure | treating polymerase as a nanopore | 16:29 |
| Juul | i wonder if it'd be possible to create a nucleotide-analog that looks like different nucleotides based on externally controlled factors. now i'm getting hand-wavy though | 16:31 |
| kanzure | yeah, in some polymerases it's watson-crick base pairing rules | 16:32 |
| kanzure | but there was one polymerase (in my paper dir) that was based on a residue that would do the matching | 16:32 |
| kanzure | instead of nucleotide-nucleotide interactions | 16:32 |
| Juul | interesting | 16:33 |
| ParahSailin__ | i would suggest using t4 polymerase as the starting point | 16:36 |
| ParahSailin__ | or something similarly small and well-characterized | 16:36 |
| kanzure | well it might be required to do a computational search of currently-known polymerase structures | 16:37 |
| kanzure | although i don't know what to look for. | 16:37 |
| Juul | hm, i remember finding a couple of papers about a human polymerase that is _very_ error prone | 16:38 |
| kanzure | is librusek the same thing as libgenesis | 16:40 |
| kanzure | http://habrahabr.ru/ | 16:42 |
| Juul | i don't think so no | 16:43 |
| Juul | i think libgenesis is only scientific information | 16:44 |
| Juul | and librusek is everything | 16:44 |
| Juul | what is habrahabr ? | 16:46 |
| kanzure | don't know yet | 16:54 |
| kanzure | http://www.reddit.com/r/trackers/comments/pv6e9/librarynu_shut_down_and_sustitutes/ | 16:54 |
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| ParahSailin__ | need a .onion service | 16:58 |
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| kanzure | jrayhawk: i'd like to do a latex+git repository on diyhpl.us, | 17:17 |
| kanzure | but it's cnoceivable some of the users will not know git | 17:17 |
| kanzure | didn't you install an ikiwiki/latex thing previously? | 17:18 |
| jrayhawk | http://ikiwiki.info/ikiwiki/directive/teximg/ Ikiwiki allows for embedded LaTeX using the [!teximg] directive. | 17:27 |
| jrayhawk | gitit uses pandoc and allows for much more flexible whatever-to-whatever conversion | 17:29 |
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| jrayhawk | http://psas.pdx.edu/KalmanIntro/ so here are some lovely TeXy equations, for example | 17:31 |
| ParahSailin__ | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2924904/?tool=pubmed | 17:31 |
| ParahSailin__ | switching time of magnet 350us | 17:34 |
| jrayhawk | http://gitit.net/Math%20Example for example features latex-to-mathml | 17:42 |
| jrayhawk | Anyway, if you want piny to support gitit, let me know. | 17:53 |
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| kanzure | jrayhawk: ideally it's something that i can export to pdf, but also visualize on the web | 18:32 |
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| kanzure | i know latex has lots of page formatting options, but presumably there's some simplification for displaying as html inside an ikiwiki template or whatever | 18:33 |
| jrayhawk | Yeah, rendering to multiple formats is definitely more a gitit thing. | 18:37 |
| jrayhawk | I don't know how pandoc deals with latex-to-html; I assume it drops most formatting altogether. | 18:38 |
| kanzure | blehh | 18:39 |
| delinquentme_ | So i think im gonna end up using py4j? | 18:46 |
| delinquentme_ | better option than deploying django in jython env | 18:46 |
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| kanzure | you could also just rewrite that java library | 18:58 |
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| kanzure | http://www.virtualdrugdevelopment.com/business1.htm | 19:04 |
| kanzure | how is this a thing? is it just made up of former biotech bigwigs and that's how they get new clients? | 19:04 |
| yashgaroth | 1998 called, they want their website back | 19:06 |
| eudoxia | sure beats the shit out of the website with just the phone number in it | 19:09 |
| yashgaroth | that's just the new modern style, very po-mo | 19:10 |
| eudoxia | ultimate minimalism | 19:10 |
| Steel2 | Thief donated to Paul. | 19:22 |
| Steel2 | Sigh. | 19:22 |
| Steel2 | *Thiel | 19:22 |
| yashgaroth | you expected different? he unironically likes seasteading | 19:22 |
| Steel2 | again, sigh | 19:23 |
| eudoxia | have these people ever been on an oilrig during a storm | 19:24 |
| eudoxia | I mean, not that I have, but still | 19:24 |
| eudoxia | expecting seasteads to look anything like the Aynrandograds they depict on the website is ridiculous | 19:24 |
| Steel2 | Man, I still stand by the ayn rand had some decent kernels of ideas in her ethics, but only if you take into account nth order self-benefit | 19:26 |
| yashgaroth | it's just an excuse for rich people to feel good about being assholes; also, people who think they'll be rich one day and want to start early | 19:27 |
| Steel2 | I'm going to be rich, and I"m already an asshole :V | 19:28 |
| * ParahSailin__ is an egoist influenced by AR | 19:34 | |
| yashgaroth | awkwaaaard | 19:37 |
| ParahSailin__ | eh | 19:38 |
| ParahSailin__ | i grew out of the zealous phase a while ago | 19:39 |
| ParahSailin__ | i dont really get thiel/seasteading -- he otherwise seems pretty macroeconomically intelligent | 19:43 |
| jrayhawk | Maybe he wants a hobby. | 19:44 |
| ParahSailin__ | probably that | 19:44 |
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| ParahSailin__ | well he threw maybe a million at the seasteading institute and it gets really cheap publicity in all the rags | 19:44 |
| yashgaroth | sleeping on a bed made of $100 bills isn't a hobby? | 19:44 |
| ParahSailin__ | but now patri left for a honduras scheme | 19:46 |
| kanzure | patri explained to me once that he didn't want seasteading inst to really do anything | 19:53 |
| kanzure | he just wanted to publish books and do media through it | 19:53 |
| kanzure | i was super disappointed when he told me that | 19:53 |
| eudoxia | I have an idea | 19:53 |
| kanzure | i think seasteading is a great thing to try but i'm disappointed that they didn't take the money seriously | 19:53 |
| eudoxia | let's take all the money from the Seasteading Inst., and give it to Dennis Chamberland | 19:54 |
| kanzure | seasteading institute probably has no more money, i bet they pay themselves | 19:54 |
| eudoxia | but then who pays for the 3D renders of Aynrandograd? | 19:54 |
| kanzure | no they have their publicity officers or whatever that they pay | 19:54 |
| kanzure | the 3d renderings were freebies because it was a competition | 19:54 |
| kanzure | iirc people submitted the renderings | 19:55 |
| eudoxia | well that sort of explains the size | 19:56 |
| eudoxia | I mean those platforms were like ~25 meters wide | 19:56 |
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| ParahSailin__ | if you're trying to decouple and isolate yourself from the "unfree" economy, why pick a place to go where you wouldnt be anywhere close to self-sufficient? | 20:04 |
| ParahSailin__ | im having a hard time seeing steel mills floating at sea | 20:05 |
| kanzure | steel mills already float at sea | 20:05 |
| kanzure | on military boats and submarines and platforms. | 20:06 |
| yashgaroth | what's the appeal over buying a bunch of land and sovereignty from some third-world country | 20:06 |
| kanzure | that's a non-issue. | 20:06 |
| kanzure | yashgaroth: show me someone who has done that | 20:06 |
| yashgaroth | gimme a billion dollars and a plane to senegal and I will | 20:06 |
| roksprok | what about oil companies? | 20:06 |
| ParahSailin__ | not a machine shop, an actual mill with blast furnaces and stuff | 20:06 |
| roksprok | they have their own security forces | 20:07 |
| ParahSailin__ | well honduras has in their recent constitution a provision for selling autonomous charter cities | 20:07 |
| ParahSailin__ | which is why patri is pursuing that option | 20:08 |
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| kanzure | ParahSailin__: wait i thought patri was pursuing a carnival thing | 20:18 |
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| * n_bentha / wrist | 20:39 | |
| kanzure | let's not | 20:40 |
| n_bentha | y not? | 20:41 |
| n_bentha | i answered on my exam that there are 50-60k gene types in the human genome because there are that many in the proteome due to alternative splicing | 20:41 |
| n_bentha | when it's like 16k gene types :( | 20:42 |
| kanzure | they might mark that wrong :/ | 20:42 |
| kanzure | yeah it's around 20k ish | 20:42 |
| n_bentha | no it's 16k gene TYPES. 20-25k genes. and 50-60k unique proteins | 20:42 |
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| kanzure | http://www.huffingtonpost.com/2012/02/15/librarynu-book-downloading-injunction_n_1280383.html | 20:53 |
| kanzure | hint: don't use your real name | 20:53 |
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| kanzure | hmm what is avaxhome | 21:05 |
| kanzure | looks like more books | 21:06 |
| kanzure | Juul: are you ok if i call the group something something enzymatic dna synthesis | 21:06 |
| Juul | kanzure, yeah definitely | 21:08 |
| Mokbortolan_ | hahaha | 21:08 |
| Mokbortolan_ | it's too late, publishers! | 21:08 |
| Mokbortolan_ | this copyright stuff is only going to get worse | 21:08 |
| Mokbortolan_ | and it'll be two things, either a police-state style of enforcement, or complete rewrite of the copyright laws | 21:09 |
| Mokbortolan_ | which do you think is more likely | 21:09 |
| kanzure | not if i launch my server fortress of terror into space first! | 21:09 |
| kanzure | actually, i bet you could raise $40M for a copyright-bypassing satellite launch | 21:10 |
| Mokbortolan_ | these organizations are already actively using law enforcement agencies, and courts, all over the world | 21:10 |
| n_bentha | what a bunch of loons | 21:10 |
| Mokbortolan_ | hiring other smaller companies to analyze filesharing traffic and identify targets | 21:10 |
| Mokbortolan_ | it'll be like Dethklok's antipiracy methods | 21:11 |
| kanzure | libraries are pretty crazy | 21:12 |
| Mokbortolan_ | next it'll move to tor | 21:12 |
| Mokbortolan_ | and then they won't have any way to control it | 21:12 |
| n_bentha | sounds like a pyramid scheme | 21:14 |
| kanzure | it's a bit worse than a pyramid scheme | 21:14 |
| n_bentha | ok we hire u guys to hire other guys to find out who's downloading the files that we sell | 21:14 |
| n_bentha | and u make them feel bad and want to buy more of our files | 21:14 |
| n_bentha | ya not really a pyramid but fuck it | 21:15 |
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| kanzure | Juul: http://groups.google.com/group/enzymaticsynthesis | 21:19 |
| kanzure | yashgaroth: ^ | 21:19 |
| kanzure | fenn: ^ | 21:20 |
| kanzure | ParahSailin__: ^ | 21:20 |
| n_bentha | 0_o what's the group for? | 21:20 |
| kanzure | thanks juul/yash | 21:20 |
| Juul | joined | 21:20 |
| kanzure | Juul: who else do you know who has explicitly expressed thoughts on this topic? | 21:20 |
| Juul | none I could name | 21:21 |
| Juul | i really need to start keeping a log of people | 21:22 |
| Juul | can anyone recommend a nice cover for the kindle? | 21:22 |
| Juul | seems like you only really need to cover the screen, and most cover the entire thing | 21:22 |
| n_bentha | my gf has a nice leather one that she uses | 21:23 |
| n_bentha | dunno the brand though | 21:24 |
| kanzure | ParahSailin__: ack how'd your name get messed up on that googlegroups page? | 21:26 |
| ParahSailin__ | my ancestors put an apostrophe in the family name | 21:26 |
| kanzure | yeah but why is googlegroups failing to display it | 21:27 |
| kanzure | ' | 21:28 |
| Juul | time-travelling sql injectors again? *sigh* | 21:28 |
| kanzure | time travel itself is an sql injector | 21:30 |
| kanzure | *injection | 21:30 |
| kanzure | fuck. | 21:30 |
| kanzure | some day i will build a time machine and fix all typos ever | 21:31 |
| Juul | and everyone will wonder why spell-checking software exists | 21:31 |
| kanzure | spell checking is just a dirty hack :P | 21:32 |
| Juul | heh | 21:33 |
| Juul | library genesis is back up | 21:33 |
| Juul | and it's pretty great | 21:33 |
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| kanzure | klafka: yo | 21:37 |
| klafka | hey | 21:37 |
| kanzure | klafka: have you and i geeked out about dna polymerase hacking before | 21:37 |
| Juul | who here is nathan? | 21:37 |
| klafka | some | 21:37 |
| kanzure | klafka: | 21:37 |
| klafka | but i'm going to sleep | 21:37 |
| kanzure | http://groups.google.com/group/enzymaticsynthesis | 21:37 |
| kanzure | i'm herding people. | 21:38 |
| yashgaroth | juul: nmz787 | 21:38 |
| kanzure | Juul: he's nmz787 when he's online (nathan mccorkle) | 21:38 |
| Juul | ah | 21:38 |
| klafka | my gf visited the over the weekend and now i'm super bummed that she's left | 21:38 |
| kanzure | her loss dude | 21:38 |
| klafka | no i mean | 21:38 |
| klafka | i don't ahve an apt | 21:38 |
| klafka | she can't move out here | 21:38 |
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| kanzure | "but if we can figure out how to | 21:53 |
| kanzure | effectively tell the polymerase "attach exactly one nucleotide now" | 21:53 |
| kanzure | then the required non-biological equipment would basically be some | 21:53 |
| kanzure | diodes with a USB interface." | 21:53 |
| kanzure | "diodes with a USB interface" is going to be my new catchphrase | 21:53 |
| kanzure | even though you're sorta right :) | 21:53 |
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| audy | kanzure: BGI github page? | 22:12 |
| kanzure | audy: um um... uhh | 22:14 |
| audy | kanzure: it's okay I can find it | 22:14 |
| kanzure | audy: https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis | 22:14 |
| kanzure | what an awful name | 22:14 |
| kanzure | why not just bgi >:| | 22:14 |
| audy | kanzure: oh I thought BGI had an OSS initiative | 22:14 |
| kanzure | hahah oh heavens no | 22:15 |
| audy | hehehe | 22:15 |
| audy | kanzure: ohnosequences.com you know them? | 22:15 |
| audy | I love the name. I'm one of my department's only bioinfortatics persons. Also, we recently got an Ion Torrent. Whenever someone sequences something they come to me next | 22:16 |
| kanzure | hrm | 22:17 |
| kanzure | nope i don't know them | 22:17 |
| audy | kanzure: they made the repo | 22:18 |
| audy | oh era7 did. So BGI outsourced to Spain | 22:19 |
| kanzure | i might have the wrong url | 22:19 |
| kanzure | this was from a slide from a bgi presentation at open science summit 2011 | 22:19 |
| kanzure | there was another github account but it seems to be taken down | 22:19 |
| kanzure | also i can't remember its name >_< | 22:19 |
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| audy | kanzure: diy bio channel is called...? | 22:28 |
| kanzure | audy: you're in it | 22:28 |
| kanzure | this is it. | 22:28 |
| audy | I thought this was posthumanism? | 22:29 |
| kanzure | what the hell is that | 22:29 |
| n_bentha | transhumanism? | 22:29 |
| audy | uploading your brains | 22:29 |
| audy | DOH | 22:29 |
| kanzure | nobody in here has uploaded any brains | 22:29 |
| kanzure | however it sounds like a cool project | 22:29 |
| audy | hehe | 22:30 |
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| kanzure | http://pr.odi.gy/ 'prodigy manifesto' | 23:28 |
| utopiah | I guess "he" made the CPU of the server that hosts this page himself too | 23:34 |
| kanzure | why not? http://code.google.com/p/homecmos/ | 23:35 |
| utopiah | I would be deeply impressed | 23:37 |
| foucist | kanzure: that's not the only way | 23:39 |
| foucist | there's homemade ocmputers out there, using wires and such | 23:39 |
| kanzure | true. ttl logic stuff. | 23:39 |
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| --- Log closed Tue Feb 21 00:00:19 2012 | ||
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