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| JayDugger | Good morning, everyone. | 00:28 |
|---|---|---|
| JayDugger | Have I missed a discussion of Venter's "synthetic life" announcement? | 00:36 |
| Utopiah | :\ | 00:47 |
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| Utopiah | JayDugger: don't worry, there is the log of the channel. | 00:54 |
| JayDugger | Ah. | 00:54 |
| JayDugger | That would mean "Yes, you did it miss the discussion," I think. | 00:54 |
| Utopiah | correct | 00:56 |
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| neobii | it's been going on for 3 days | 01:04 |
| JayDugger | Conclusions? | 01:17 |
| JayDugger | Major viewpoints? | 01:17 |
| JayDugger | Flame? | 01:17 |
| Utopiah | 2012. | 01:17 |
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| JayDugger | 2012 for what? End of the Drug War, as Some argue; Collapse of OPEC when Venter and Exxon get algae ponds to crap out gasoline; End of Archer-Daniels-Midland when we'll all eat ultra-spirulina & super-chorella from backyard ponds? | 01:28 |
| JayDugger | And what's the URL for the log? :) | 01:28 |
| klafka | JayDugger, it's a whole lot of fucking hype | 01:28 |
| JayDugger | Ahh...much better. | 01:29 |
| klafka | for something that has some interesting technical challenges but isn't the revolution that people are making it | 01:29 |
| JayDugger | Thanks, that answers my main question. | 01:29 |
| klafka | it's not synthetic life, it's the establishment of techniques to synthesize a long contiguous strand of DNA taht we can inject into an existing cell | 01:29 |
| JayDugger | Yes, I got that from the AAAS podcast. | 01:30 |
| klafka | what's the AAAS? | 01:32 |
| Utopiah | http://www.aaas.org/ | 01:32 |
| klafka | aah | 01:33 |
| Utopiah | (Powerslide Into Parking Spot http://www.youtube.com/watch?v=RY93kr8PaC4 Stanford) | 01:40 |
| Utopiah | (Andrew Hessel - The Internet of Living Things http://www.youtube.com/watch?v=S23owdOuLjc momo Amsterdam April 2010) | 02:00 |
| Utopiah | ( http://fora.tv/live/maker_faire/Maker_Faire_2010 (live 11:00 AM PDT)) | 03:23 |
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| kanzure | "the internet of living things" ha, ha | 09:12 |
| kanzure | i should hit him for that | 09:12 |
| kanzure | he's in town in 2 days from now | 09:12 |
| Utopiah | http://linux06.dnspropio.com/~fusionvic/ diy reactor for fusion energy production | 09:49 |
| wilywonka | lol yah | 10:00 |
| wilywonka | like anyone has diy'd that | 10:00 |
| wilywonka | just the tube with grooves alone would be super difficult | 10:02 |
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| Utopiah | don't remember who asked about protocols last time but there is in addition to Springer website http://www.currentprotocols.com/ (with a package on bitme.org ) | 10:42 |
| Utopiah | (sidenote : I gathered those and few others at http://fabien.benetou.fr/ReadingNotes/ElegantSolutions#ExperimentsTools ) | 10:50 |
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| thesnark | kanzure you there? | 11:05 |
| kanzure | sort of | 11:15 |
| Utopiah | http://www.deshawresearch.com/computational biochemistry under the direct scientific leadership of David Shaw | 12:01 |
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| klafka | A former faculty member in the computer science department at Columbia University, Shaw made his fortune exploiting inefficiencies in financial markets with the help of sophisticated computer models. | 12:16 |
| klafka | weird | 12:16 |
| Utopiah | arbitrage | 12:17 |
| klafka | yeah | 12:18 |
| kanzure | etacts.com is hiring | 12:40 |
| kanzure | fenn: they are in the palo alto area. you should show up and show off your data. | 12:40 |
| kanzure | they are python mongers, too | 12:40 |
| wilywonka | what does he do with python? | 12:50 |
| kanzure | etacts.com? well it's a website | 12:50 |
| wilywonka | no fenn or whoever | 12:50 |
| kanzure | and they claim they're using django | 12:50 |
| kanzure | uh i don't know how to answer that | 12:50 |
| kanzure | stuff, ok? | 12:51 |
| wilywonka | i was under the impression not many ppl here did bioinformatics type stuff | 12:51 |
| wilywonka | lol | 12:51 |
| kanzure | half of us do | 12:51 |
| * kanzure me | 12:51 | |
| * Utopiah kinda uses etacts too | 12:51 | |
| wilywonka | well have you ever tried compiling popular genefinders | 12:51 |
| kanzure | Utopiah: i stopped using it pretty much immediately | 12:51 |
| kanzure | but their heart is in the right place i guess | 12:52 |
| wilywonka | like I find genefinders pretty interesting but i guess maybe they're useless cos there hasn't been loads of improvement since say 2005 or so | 12:52 |
| Utopiah | yep | 12:52 |
| wilywonka | like i think on the human genome they're largely irrevelant cos there are at least enough researchers to annotate every gene | 12:52 |
| kanzure | updated: http://designfiles.org/~bryan/meetlog/meetlog.txt | 12:53 |
| wilywonka | so are you running for president | 12:55 |
| * Utopiah have a wiki page on that :-# | 12:56 | |
| wilywonka | i mean that's pretty interesting but also can you really usefully know 1,000s of people | 12:56 |
| Utopiah | (Project SOAP http://project-soap.eu/ Study of Open Access Publishing ) | 13:12 |
| wilywonka | umm why would you name it soap | 13:14 |
| wilywonka | they're been a few articles about that in nature recently | 13:14 |
| wilywonka | the main problem that was brought up | 13:15 |
| wilywonka | was that quality of reviews would suffer | 13:15 |
| wilywonka | and at the current rates of publication reviews are essential | 13:15 |
| wilywonka | there are no ways you could read everything | 13:15 |
| wilywonka | and often invited reviews are written by people more respected in their field than the average original research paper | 13:16 |
| Utopiah | (looks like a nice blog http://www.academicproductivity.com/ overall) | 13:16 |
| wilywonka | seeing how they named that soap though makes me wonder how often academics keyword stuff, i often read papers where it seems like that is what is going on as they say something 5 ways and it doesn't seem like a concept that needs to be drilled into your head | 13:19 |
| wilywonka | i mean that almost seems like a form of keyword stuffing naming your project after a search term that gets tons of searches | 13:20 |
| Utopiah | I think at the European research program level they dont care, they make acronyms and they make the norm. | 13:20 |
| Utopiah | it's a gigantic adminstrative machine | 13:20 |
| wilywonka | yeah that's probably true but still a horrible acronym could've thought of a better one easily or just not made it an acronym | 13:20 |
| Utopiah | they make acronyms for nearly every project and I suppose they actually have a tool for that | 13:21 |
| Utopiah | at least a process | 13:21 |
| Utopiah | they're not here for the marketing ;) | 13:22 |
| Utopiah | I mean it's anything but an agile startup | 13:22 |
| wilywonka | but anyway on the other hand it does seem odd that research funded by taxpaper money eventually culminates in a peer reviewed journal that i'm sure only an infinitesimal portion of the taxpayers have access to, so in that regard obviously open access could be the only way of the future, i guess its just about how do you get there from here | 13:25 |
| klafka | i di bioinformatic stuff! | 13:27 |
| klafka | i think open access is the way forward atm | 13:27 |
| wilywonka | what do you say about the point of reviews though | 13:27 |
| wilywonka | for instance nature reviews series are great website is great just plain great | 13:27 |
| klafka | it is | 13:27 |
| klafka | but I don't see why you can't have an OA review journal | 13:28 |
| wilywonka | bioessays is pretty good but way harder to use | 13:28 |
| wilywonka | well its mainly that there isn't a financial incentive to do reviews i'm sure | 13:28 |
| wilywonka | and also reviews need to be invited | 13:28 |
| wilywonka | instead of anyone do them | 13:28 |
| wilywonka | if anyone did them they'd sorta be like bioinformatics is now | 13:28 |
| klafka | so the main problem si that people won't pay to submit a review | 13:28 |
| wilywonka | where any who wants to just chunks out some probably useless information | 13:29 |
| wilywonka | no no some people definitely would | 13:29 |
| Utopiah | know the price of http://www.plosbiology.org/ ? | 13:29 |
| klafka | but they wouldn't be invited so the quality would suffer | 13:29 |
| wilywonka | its about 3500 i think | 13:29 |
| klafka | per page? | 13:29 |
| wilywonka | not sure | 13:29 |
| Utopiah | not really one of the cheapest to publish in | 13:29 |
| klafka | granting agencies particularly the NIH expect you to build OA journal publication into your budgets though | 13:30 |
| klafka | iirc | 13:30 |
| wilywonka | anyway people would pay to write reviews | 13:30 |
| wilywonka | i have no doubt of that | 13:30 |
| wilywonka | i mean publish or perish | 13:30 |
| klafka | yeah but reviews count for nothing | 13:30 |
| klafka | in terms of publications | 13:30 |
| wilywonka | ppl would write reviews cos in ways it might be easier | 13:30 |
| wilywonka | is that really the case i thought impact factor was everything | 13:30 |
| klafka | i think the two ways to avoid the issue, setup a respectable, moderated wiki | 13:30 |
| wilywonka | and often reviews can have a high impact factor | 13:31 |
| klafka | wilywonka, reviews have no impact | 13:31 |
| klafka | at least that's what everyone tells me | 13:31 |
| wilywonka | oh ok well i only have access to scopus anyway | 13:31 |
| klafka | most of them are "written" by well known people, but they are actually written by their grad students | 13:31 |
| wilywonka | don't have wok or whatever its called now | 13:31 |
| klafka | i don't have either of those, just everyone tells me that no one cares about seeing what review papers you've written | 13:32 |
| klafka | my program director, my advisors, anyone i've talked to | 13:32 |
| wilywonka | well i often see them as the highest cited papers | 13:32 |
| wilywonka | so that's where i was drawing from | 13:32 |
| klafka | right but they aren't original works | 13:32 |
| klafka | ah | 13:32 |
| wilywonka | seems like you're probably right but it might be a biology only phenomena | 13:33 |
| klafka | i think you could get around a lot by establishing a fund for the publication of OA reviews that would invite people, or I thin really the way to move forward is to abandon the journal model altogether | 13:33 |
| klafka | and go to a "wiki-like" model | 13:33 |
| wilywonka | i mean i'd assume in more theoretical fields the line between review and original gets more blurred | 13:33 |
| klafka | yeah | 13:33 |
| wilywonka | also one of the best things about reviews is they often have graphics that are understandable | 13:34 |
| wilywonka | often in a good review you could look at just the figures and captions and understand most of the points | 13:34 |
| klafka | well it's sort of weird, like i'm in boht biology and CS (my 1 advisor is more biology, my other is machine learning) and like reviews/technical reports seem to be done by the best | 13:34 |
| wilywonka | i'm pretty sure nature for instance has no problem hiring ppl to make the graphics | 13:35 |
| wilywonka | as they figure some of them they'll reuse in a textbook | 13:35 |
| klafka | but they dn't count for anything because by the time you do big reviews you're already established | 13:35 |
| klafka | i wasnt aware that nature actually made any graphics for the reviews | 13:36 |
| wilywonka | well i'm assuming that | 13:36 |
| wilywonka | but they're all the same color scheme etc | 13:36 |
| wilywonka | in almost all the reviews | 13:36 |
| klafka | idk well we can check | 13:36 |
| wilywonka | and i figured since owned by macmillan | 13:36 |
| wilywonka | maybe that's assuming they're more efficient than they really are though | 13:37 |
| klafka | my school doesn't have nature review genetics and it's incredibly irritating | 13:38 |
| klafka | i must say | 13:38 |
| wilywonka | you can't get it through the proxy at all | 13:38 |
| wilywonka | ezproxy | 13:38 |
| klafka | ah you are in fact correct wilywonka | 13:39 |
| klafka | ? Artwork. The figures in the Nature Reviews journals are all constructed (or redrawn) in house, in consultation with the author. Authors are encouraged to send rough drafts of figures early in the writing process. | 13:39 |
| wilywonka | yeah so my assumption was they have financial incentive to do good work there | 13:39 |
| wilywonka | cos they will reuse it in a textbook | 13:39 |
| wilywonka | and that makes sense and also explains how they can consistently be good quality which they are (although sometimes they do not make any sense ..... like a textbook) | 13:40 |
| klafka | heh true | 13:40 |
| wilywonka | so like for instance for the diy ppl | 13:41 |
| wilywonka | they have limited resources just as everyone does | 13:41 |
| wilywonka | probably even less than someone in the field | 13:41 |
| wilywonka | so to maximize their time they would probably rather read a review (as say their main source of information on their subject of interest) | 13:42 |
| wilywonka | so an open access review would probably do way more good than just open access research articles | 13:42 |
| wilywonka | i mean most people who are in the field (excluding corporate work) already have access | 13:43 |
| wilywonka | i mean i guess pnas is just what i'm argueing for | 13:43 |
| kanzure | wilywonka: i have some software for "really usefully knowing" 1,000s of people | 13:43 |
| wilywonka | kanzure: yeah i was noticing on your site | 13:44 |
| wilywonka | klafka: http://www.pnas.org/content/early/recent i mean them open accessing some articles there is pretty useful as pnas articles aren't always necessarily reviews but often are in the spirit of a review in ways | 13:45 |
| wilywonka | but they only do a few articles oa | 13:45 |
| klafka | yeah i think their OA articles are submitters choice | 13:46 |
| wilywonka | but unlike a science paper | 13:46 |
| wilywonka | the average intelligent person could understand a pnas article | 13:46 |
| wilywonka | so what kind of bioinformatics stuff do you do | 13:51 |
| wilywonka | i was looking at gene finders and well i think that's a bit over my head | 13:51 |
| wilywonka | but i do find it crazy that we really can't predict all eukaryotic genes and further that we can't accurately predict all the splice sites | 13:52 |
| klafka | i am interesting in learning biological networks | 13:52 |
| wilywonka | and then we have to rely on est sequencing to really tell which parts are genes | 13:52 |
| wilywonka | as in systematics type work | 13:52 |
| Utopiah | (gene finders like http://www.ncbi.nlm.nih.gov/gene ?) | 13:52 |
| klafka | yeah | 13:52 |
| wilywonka | as in you have a new sequenced genome | 13:53 |
| klafka | improving graphical models of regulatory networks from heterogenous data types | 13:53 |
| wilywonka | denovo sequenced genome | 13:53 |
| wilywonka | and you want to predict all the genes that exist in that genome | 13:53 |
| klafka | yeah | 13:53 |
| wilywonka | and want high accuracy | 13:53 |
| klafka | they do that a lot w/ metabolic network reconstruction tools | 13:54 |
| wilywonka | for instance in the human genome this isn't super relevant | 13:54 |
| klafka | like pathway finder | 13:54 |
| wilywonka | because there are literally thousands of researchers | 13:54 |
| wilywonka | maybe enough to ensure that stochiastically one is "likely" to investigate every known est | 13:54 |
| klafka | well a lot of the human genome is largely mapped out | 13:54 |
| wilywonka | what do you mean heterogenous data types | 13:55 |
| wilywonka | as in heterogenous alleles/genes/haplotypes | 13:55 |
| klafka | like most regulatory network models use gene expression data like microarrays or RNA-seq | 13:55 |
| wilywonka | oh ok so intergrating different types of data | 13:56 |
| klafka | but because the # of samples needed to lower variance is cost prohibitive you need to integrate in other data types | 13:56 |
| klafka | PPI, metabolic networks, genotype data, etc... | 13:56 |
| wilywonka | that sounds like a pretty complex system | 13:57 |
| klafka | well you sort of abstract the complexity out of it | 13:57 |
| klafka | like so instead of being a complex weird simulation, necessarily, you use this existant data to say regularize your model | 13:58 |
| wilywonka | how tissue dependent can the models be | 13:58 |
| klafka | basically we have a large corpus of data available to us that is not designed for our uses, but we can make it | 13:58 |
| klafka | at this moment there are very few people acting on anything other than prokaryotes or yeast | 13:58 |
| klafka | because the answer is, each tissue (and cell type) is going to have sort of custom regulatory networks based on stuff like chromatin structure, methylation, etc... | 13:59 |
| wilywonka | yeah | 13:59 |
| * Utopiah doesn't know a lot on that topic but isn't afraid of asking silly questions | 14:00 | |
| wilywonka | for instance i imagine a world where we basically have a computer emulator of the basic genetic rules as they evolved in divergent lineages that you could say insert a genome sequence and basically know alot about what that organism looked like | 14:00 |
| klafka | go for it | 14:00 |
| Utopiah | regarding gene finders, are they using phylogenetic tree to limit the search space and optimize queries? | 14:00 |
| wilywonka | some do | 14:00 |
| wilywonka | some can only find one intron | 14:00 |
| wilywonka | some can find multiple | 14:01 |
| wilywonka | but see phylogenetic trees aren't necessarily a good answer | 14:01 |
| klafka | willywonka well i think what will happen iis sequencing will get so cheap and automated we actually wil lbeable to get the amount of high throughput data we actually need | 14:01 |
| wilywonka | like in yeast | 14:01 |
| wilywonka | there is a divergent clade that uses a different codon set | 14:01 |
| wilywonka | and so that might be an easy case to realize hey our model is wrong, but still it can't account for that just in the finder itself | 14:02 |
| wilywonka | well yeah i mean obviously the next step in regulatory networks will be you | 14:02 |
| wilywonka | you'll get a paired dataset of est from various tissues along with full genome | 14:02 |
| Utopiah | out of curiosity, did any of you subscribed to 23andMe and why? | 14:03 |
| wilywonka | nah i didn't | 14:03 |
| Utopiah | too low resolution? | 14:03 |
| Utopiah | privacy? | 14:03 |
| wilywonka | heh privacy | 14:03 |
| wilywonka | aren't they familialy owned by google basically | 14:03 |
| klafka | sort of | 14:03 |
| wilywonka | founders wife owns 23andme | 14:03 |
| klafka | i actually saw a tlak aby an engineer of 23andme | 14:04 |
| wilywonka | forget which one but yah | 14:04 |
| klafka | and one of the co-founders of it | 14:04 |
| klafka | what really turned me off is that they said they are likely to patent any important genes they find | 14:04 |
| wilywonka | everyone does that | 14:04 |
| wilywonka | i mean craig venter tried patenting like 200 or something in his project | 14:04 |
| klafka | academic institutions do not | 14:04 |
| klafka | craig venter's kind of a jerk too :P | 14:04 |
| Utopiah | wasn't that kicked out few weeks ago in the US by the patent office? | 14:05 |
| klafka | well it was overturned in a lower court | 14:05 |
| klafka | but i'm sure it'll go to the supreme court | 14:05 |
| wilywonka | not sure | 14:05 |
| wilywonka | i liked michael creighton's views on it | 14:05 |
| wilywonka | he had that fiction book on the subject | 14:05 |
| klafka | anyway i better go tkae a shower bbl | 14:06 |
| wilywonka | and some good essays in the appendix like section | 14:06 |
| Utopiah | (somebody in the channel was stinky and didn't do anything about it...) | 14:06 |
| Utopiah | http://www.crichton-official.com/ ? | 14:06 |
| wilywonka | yeah so i guess his last book? | 14:07 |
| wilywonka | let me find you that list of gene finders i had | 14:08 |
| Utopiah | the last related books I read on that was probably The Biotech Century - Jeremy Rifkin ... a decade ago | 14:09 |
| wilywonka | http://geneprediction.org/ | 14:14 |
| wilywonka | anyway some of those might take you all day to compile if you could at all | 14:14 |
| wilywonka | some require programs you have to email to get access to ( i assume so you cite them) | 14:15 |
| Utopiah | CiteWare ;) | 14:15 |
| wilywonka | haha | 14:15 |
| wilywonka | anyway like the frog genome just published in science they used just 2 | 14:16 |
| kanzure | Hmm wait a second | 14:16 |
| kanzure | i thought cody marx bailey claimed he invented hashtags? | 14:16 |
| kanzure | another guy is claiming the same thing here: | 14:16 |
| kanzure | http://code.google.com/events/io/2010/speakers.html | 14:16 |
| kanzure | chris messina: "Chris got his start in 2004 by leading community marketing through the launch of Firefox. He is a board member of the OpenID and Open Web Foundations and plays an instrumental role in advancing OAuth and safer online computing. In 2008, Chris received the Google Open Source Award recognizing his community work on initiatives like microformats. He also co-founded the coworking and BarCamp communities and introduced hashtags on | 14:16 |
| wilywonka | anyway the thing that makes gene prediction more interesting is that you could use it to predict genes that are alternatively spliced or maybe to recognize variants that have a higher probability to be alternatively spliced | 14:19 |
| wilywonka | in eukaryotes we've constantly learned that there are lots of places where even a synonymous mutation can drastically change how it is expressed | 14:20 |
| klafka | also i have a feeling de novo assembly and gene prediction when 3rd gen sequencers become popular will get a lot easier | 14:25 |
| wilywonka | why would it | 14:25 |
| klafka | because they have really really long read lengths | 14:25 |
| wilywonka | oh is that what 3rd generation is ha | 14:25 |
| klafka | like atm pac bio has avg read lengths of like 1000-1200~ with max of ~20,000 | 14:26 |
| wilywonka | i thought some were supposed to be even lower | 14:26 |
| klafka | i suppose it depends on the 3rd gene sequencer | 14:26 |
| klafka | 3rd gen at this point means "single molecule sequencing" | 14:26 |
| klafka | pretty much | 14:26 |
| wilywonka | i think some ppl consider their technology 3rd gen cos of thoroughput | 14:26 |
| wilywonka | but yeah long reads would help tons | 14:26 |
| klafka | yeah the terms are nebulous and ill-defined | 14:27 |
| klafka | but like for instance illumina's Hi-Seq isn't 3rd gen by most people's standards | 14:27 |
| klafka | though it's really fast | 14:27 |
| wilywonka | in some areas it could just be you can't predict the gene cos of the sequencing errors | 14:27 |
| wilywonka | or other sequencing errors in other places messing up the model | 14:27 |
| wilywonka | i'd consider that a top priority though i mean how can you engineer a genome when you don't even really know what sequences will code | 14:28 |
| wilywonka | i mean with the ghmm's you don't really know all the features that will do something but if you could distill the hidden model into a thought out and rationale model you might know something | 14:29 |
| wilywonka | did you see the alternative splicing paper in this month's nature | 14:32 |
| wilywonka | well in a nature this month | 14:32 |
| wilywonka | http://www.nature.com/nature/journal/v465/n7294/full/nature09000.html | 14:35 |
| wilywonka | http://genes.toronto.edu/wasp/ | 14:36 |
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| Utopiah | (regarding SPOF http://www.neustar.biz/ seems like a good target) | 14:51 |
| Utopiah | (according to http://www.theatlantic.com/magazine/archive/2010/06/the-enemy-within/8098/ at least) | 14:51 |
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| Utopiah | (regarding earlier mention on 23andMe http://www.pbs.org/wgbh/nova/sciencenow/0406/01.html ) | 15:40 |
| Utopiah | (and http://www.personalgenomes.org/ ) | 15:41 |
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| QuantumG | someone asked me what a transhumanist is last night | 15:46 |
| wilywonka | james watsons' ghostwritten book had a good section on it | 15:46 |
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| wilywonka | he compared the 3 or 4 companies that do that personal genomics | 15:47 |
| QuantumG | I said "someone who recognizes the human condition can be improved and works to achieve that goal for themselves." | 15:47 |
| QuantumG | and this morning I found this video http://vimeo.com/8977365 pretty neat little documentary | 15:48 |
| wilywonka | on http://www.pbs.org/wgbh/nova/sciencenow/0406/01.html i like that graphic ha | 16:03 |
| wilywonka | on the edge.org talk someone mentioned that sydney brenner was "reading" the human genome | 16:04 |
| wilywonka | and craig venter was like well good luck with that it would take you about x ridiculous amount of years | 16:04 |
| wilywonka | i guess 9.5 | 16:05 |
| QuantumG | "Thousands of people are signing up to post their DNA sequences on the Internet, for all to see. Are they crazy?" That basically sums up the moronic level of public discourse on genomics | 16:09 |
| bkero | I've got some A's, G's, T's, and C's, should I put them on the internet? | 16:11 |
| kanzure | i have a few clients who are super super shady about privacy and genomics | 16:11 |
| kanzure | like, they pay extra for it to be kept private | 16:11 |
| kanzure | shipping fucking genomes in fucking granite boxes | 16:11 |
| kanzure | god damn it | 16:11 |
| kanzure | (can you tell i am upset?) | 16:12 |
| Utopiah | (now yes) | 16:12 |
| QuantumG | no, tell us what you really feel | 16:12 |
| QuantumG | every time I hear people talk about the 3 billion bps in a human genome I imagine what it would be like if I counted the number of characters in my work's source code and referred to that repeatedly | 16:17 |
| QuantumG | I can get to 3 billion pretty damn quickly. | 16:18 |
| kanzure | i should just hire someone to follow those guys around with cotton swabs | 16:22 |
| kanzure | and steal dna from trash. | 16:22 |
| kanzure | "put *that* in a granite box." | 16:22 |
| QuantumG | immaculate workspace indeed | 16:23 |
| klafka | QuantumG, is that about personalgenome ? | 16:27 |
| QuantumG | http://www.pbs.org/wgbh/nova/sciencenow/0406/01.html is | 16:27 |
| QuantumG | http://vimeo.com/8977365 is about the blue brain project | 16:27 |
| kanzure | klafka: have you heard of the blue brain project? | 16:28 |
| klafka | yep | 16:28 |
| QuantumG | btw, are they still saying about 20,000 genes in the human genome? To me, that sounds like about the same as a class list in software. | 16:28 |
| klafka | what's a gene? | 16:28 |
| kanzure | says the bioinformatician :) | 16:28 |
| QuantumG | their definition is probably something like, a unique reading between a start and a stop codon, multiplied by alternate splicings. | 16:29 |
| kanzure | http://designfiles.org/~bryan/chats/bioinformatics.txt | 16:29 |
| Utopiah | klafka: it's like a meme in biology ;) | 16:30 |
| klafka | lol | 16:30 |
| klafka | thanks Utopiah | 16:31 |
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| Utopiah | np, Im sure it helps a lot | 16:31 |
| klafka | speaking of this, you guys wanna see my company logo ? since this is #hplus http://imgur.com/oDyER | 16:31 |
| klafka | it's fitting | 16:31 |
| kanzure | what company | 16:31 |
| klafka | it's a music promotion company | 16:31 |
| kanzure | i really like this diybio promo poster: http://designfiles.org/~bryan/images/diybio_promo.png | 16:32 |
| klafka | hahah | 16:33 |
| klafka | yeah i liek that too | 16:33 |
| wilywonka | @ quantumG 3 billion bp...... but do you have an obfuscated perl script that is 3 billion chars long? | 16:33 |
| wilywonka | if so i'd be impressed | 16:33 |
| kanzure | i wouldn't be :( | 16:33 |
| kanzure | perl is naturally obfuscated | 16:34 |
| wilywonka | yeah but it'd be like a 1gb + one line perl script | 16:34 |
| QuantumG | I've been pulling my hair out over doing security analysis of php.. if they give me perl to do next I quit | 16:34 |
| kanzure | "security analysis" of php | 16:34 |
| kanzure | heh | 16:34 |
| QuantumG | yeah I know, just say "dude, you're using php" and flag it as critical | 16:34 |
| kanzure | i like my broken window theory of php | 16:35 |
| kanzure | well, it wasn't mine before | 16:35 |
| kanzure | but i've adopted it now :) | 16:35 |
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| QuantumG | btw http://www.xkcd.com/743/ | 16:38 |
| QuantumG | fucking gold | 16:38 |
| parolang | QuantumG: You gonna quit facebook on 5-31? | 16:40 |
| klafka | haha | 16:40 |
| kanzure | 5/31 is a quit date for facebook? | 16:40 |
| QuantumG | parolang: not on facebook | 16:40 |
| parolang | kanzure: yeah | 16:40 |
| kanzure | parolang: link? | 16:40 |
| QuantumG | for the reasons outlined in the comic no less :) | 16:40 |
| parolang | http://www.quitfacebookday.com/ | 16:41 |
| QuantumG | that, and, well, it's "social networking" not "anti-social networking" | 16:41 |
| kanzure | hah | 16:41 |
| kanzure | QuantumG: i think there's an anti social networking website | 16:41 |
| QuantumG | yeah, it's called Slashdot | 16:42 |
| kanzure | it's called irc | 16:43 |
| kanzure | now get off my bits | 16:43 |
| * parolang wonders if people even know about IRC anymore. | 16:44 | |
| kanzure | quitfacebookday.com should get on kickstarter to raise funds to advertize on facebook about quitting facebook | 16:45 |
| QuantumG | nice | 16:45 |
| kanzure | since it's in the interest of people with money to have them get off facebook | 16:45 |
| parolang | I've been thinking about quitting facebook for some time now, I'll decide by 5-31 :) | 16:47 |
| parolang | But then, I haven't been on it very long. | 16:47 |
| parolang | QuantumG should join Facebook in order to quit on quit facebook day. | 16:47 |
| kanzure | i wonder if i can delete my dad's account on facebook | 16:48 |
| kanzure | it's kind of sad. he signed up the day before he died | 16:48 |
| kanzure | so i'm his only friend :/ | 16:48 |
| parolang | :( | 16:48 |
| Utopiah | :| | 16:48 |
| Utopiah | saddest thing Ive heard today, guess I can't go to sleep just now... | 16:49 |
| * parolang wonders how many deceased users are on facebook. | 16:49 | |
| kanzure | it probably matches the national death rate or average death rate for the world over | 16:49 |
| kanzure | adjusted for the average facebook user age range (40 to 50?) | 16:50 |
| Utopiah | kanzure: my 2cents, delete both and move on. | 16:50 |
| parolang | I'd think that the facebook crowd probably leans a bit younger than that. | 16:50 |
| parolang | Probably mostly people who were in college when facebook became popular. | 16:51 |
| kanzure | i have a friend with a ridiculously low id number (4 digits) | 16:51 |
| kanzure | and i investigated one time | 16:51 |
| kanzure | and it turns out he went to harvard | 16:52 |
| kanzure | soo that would explain it | 16:52 |
| * parolang has a five digit slashdot id :) | 16:52 | |
| wilywonka | i have a myspace with 3 digits | 16:52 |
| wilywonka | i got it from an exploit though | 16:52 |
| parolang | Heh, I never gave myspace the time of day. | 16:52 |
| parolang | Slashdot is weird...I rarely post, and when I do I usually get mod points the following day or two. | 16:53 |
| wilywonka | i used to have the aim texas before it got suspended | 16:53 |
| parolang | I just go through and mod QuantumG's posts and call it a day. | 16:54 |
| kanzure | yeah who is that QuantumG guy anyway | 16:54 |
| kanzure | >_< | 16:54 |
| parolang | :) | 16:56 |
| parolang | Wow...Pandora is being released finally :) | 16:57 |
| * parolang will stop reading slashdot headlines. | 16:57 | |
| klafka | which pandora? | 16:58 |
| parolang | The game console | 16:58 |
| kanzure | about time. | 16:58 |
| parolang | no kidding, I thought it was vaporware | 16:59 |
| QuantumG | parolang: up or down? :) | 17:01 |
| parolang | QuantumG: Which direction have your posts been modded lately? | 17:05 |
| QuantumG | up, today | 17:06 |
| parolang | Well, what about yesterday? | 17:06 |
| kanzure | http://moanmyip.com/ yess | 17:06 |
| kanzure | (NSFW) | 17:07 |
| parolang | Actually, I kid. I don't actually use mod points very much :) | 17:07 |
| parolang | Slashdot has been lame for a while now, but I keep going there. I should spend more time on lwn.net, buy a subscription, etc. | 17:07 |
| kanzure | http://news.ycombinator.com/best can be ok at times | 17:08 |
| kanzure | but it's a hype gravy train :/ | 17:09 |
| parolang | I feel like I shouldn't be there because I don't have a startup :) | 17:09 |
| kanzure | tell that to everyone else there | 17:10 |
| parolang | heh | 17:11 |
| wilywonka | i think i like reddit best esp the slower moving views | 17:16 |
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| wilywonka | i feel like i actually read neat stuff instead of waste time on reddit | 17:16 |
| wilywonka | i mean i guess they're the same thing but not completley | 17:16 |
| parolang | reddit has it's virtues | 17:17 |
| wilywonka | yeah its pretty good just avoid all or wtf if you don't wanta waste tons of time | 17:18 |
| parolang | But, you know, as far as content these sites aren't too different (lwn I think does higher quality there), usually the hype feeds all of them. The difference is mainly the users. That's what made slashdot cool back when it was cool, you had people who knew what they were talking about commenting in the threas. Today, I end up facepalming too much :) | 17:19 |
| kanzure | some say metafilter is still worth your time | 17:21 |
| parolang | You know, a good news aggregater is any mailing list kanzure happens to be on :) | 17:25 |
| wilywonka | lol | 17:27 |
| wilywonka | oh man i used to read bloglines | 17:27 |
| wilywonka | well used to use it to read feeds | 17:27 |
| wilywonka | but realized that was a waste of time | 17:28 |
| wilywonka | even ppl i honestly like their blogs are well tl;dr | 17:28 |
| klafka | lol | 17:28 |
| klafka | parolang, lol kanzure are you on extropy? | 17:29 |
| parolang | yeah, and om | 17:29 |
| kanzure | well i'm glad at least one person is getting something out of my emails | 17:42 |
| parolang | I'm sure lots of people are; you're basically doing what hacker news and reddit do on a smaller scale. | 17:44 |
| kanzure | i was really surprised when nobody replied to the email about the defensive patent license idea | 17:45 |
| parolang | Well, I don't usually post at all, and don't check all the mailing lists regularly. | 17:47 |
| kanzure | i hate how people keep making new mailing lists :( | 17:49 |
| parolang | Hmm...there might be a technical reason for that though. | 17:51 |
| parolang | Just in the sense that it's easy to create a new ML or delete and existing ML; but the operations of splitting a ML into two, or combining two MLs into one, are missing or difficult (or go against conventional rules of etiquette). | 17:53 |
| wilywonka | lol | 17:53 |
| wilywonka | that is true but that is probably a very altruistic reason for why they create new ones | 17:54 |
| parolang | principle of charity :) | 17:54 |
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| QuantumG | the principle of charity is one that I'd love to be on the Arguing On The Internet License, should they ever introduce one | 17:57 |
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| wilywonka | from reddit: Every time I see Pearson, et al. cited in a paper after the first mention of the word FASTA, I think of a real smug old man who smokes his pipe and thinks, "Using a greater-than sign to indicate metadata for a sequence... that was me." | 18:28 |
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| parolang | http://www.insidefacebook.com/2009/02/02/fastest-growing-demographic-on-facebook-women-over-55/ | 19:37 |
| parolang | Demographic information about facebook...we were talking about it briefly earlier. | 19:37 |
| wilywonka | lol http://www.splicethefilm.com/ | 19:50 |
| wilywonka | i'm sure that's gonna make the crazies even crazier | 19:50 |
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| wilywonka | also i kinda wonder about facebook demographics | 20:49 |
| wilywonka | cos once it got big ppl but way more efforts into making bots | 20:49 |
| wilywonka | and the majority of bots are likely to be women | 20:49 |
| wilywonka | i mean maybe someone did rand(0,100) on age but regardless i'd take info like that with a grain of salt unless you knew exactly how well it was filtered | 20:50 |
| kanzure | eyewriter from techcrunch disrupt for playing mario :) http://www.youtube.com/watch?v=eMNtrLcbCNk | 21:46 |
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| fenn | ug. | 22:54 |
| kanzure | fenn: the rest of the iphone team wants me to start coming in to work | 23:02 |
| kanzure | :/ | 23:03 |
| kanzure | for programming | 23:03 |
| kanzure | what's your opinion? do i do better coding in person or over the net | 23:09 |
| fenn | my opinion is that you should go in to make them happy | 23:41 |
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