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| kanzure | beep boop | 08:15 |
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| kanzure | http://mailinator.blogspot.com/2012/02/how-mailinator-compresses-email-by-90.html | 09:39 |
| kanzure | neat. i don't know what i would do without mailinator :x | 09:39 |
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| kanzure | "owell has a "suitcase lab" for biohacking on the go. As well as a mini gel electrophoresis kit by Invitrogen, you can cram in a thermocycler, dishes and pipettes. The tricky part is cold storage: "You might need a separate pouch with a cold pack in it," he advises." | 10:29 |
| kanzure | hmmm i haven't seen this alleged suitcase lab | 10:29 |
| Mokbortolan_ | why... would you need a suitcase biohacking lab... | 10:30 |
| uniqanomaly__ | so you could do science on the shitter | 10:31 |
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| audy | you could attach microcentrifuge tubes to the spokes of a bicycle and centrifuge them as you commute to wherever it is you plan on suitcase biohacking | 11:14 |
| Mokbortolan_ | you could tie vials to your socks to agitate them as you walk :p | 11:15 |
| audy | suit lab for biohacking on the go | 11:15 |
| audy | for biohacking super{hero,villian}s | 11:16 |
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| delinquentme | ChemicalStructure inchi = ne.getFirstChemicalStructure(FormatType.INCHI); translating this bit of java | 15:30 |
| delinquentme | into Ruby | 15:30 |
| delinquentme | inchi = ne.getFirstChemicalStructure(FormatType.INCHI) << not _quite_ | 15:30 |
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| kanzure | Juul: how's your tex-fu | 15:46 |
| Juul | kanzure, very basic | 16:00 |
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| delinquentme | dude jruby | 16:08 |
| delinquentme | is beautiful | 16:08 |
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| kanzure | Q01529 "Probable DNA polymerase" | 16:48 |
| kanzure | http://www.uniprot.org/uniprot/Q01529 | 16:48 |
| kanzure | "This DNA polymerase requires a protein as a primer" | 16:49 |
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| Juul | interesting | 17:05 |
| Juul | but this protein hasn't been studied directly | 17:10 |
| Juul | it says "inferred from sequence homology" | 17:10 |
| Juul | so there must be some other protein that _has_ been studied, with a similar sequence | 17:11 |
| Juul | though i'm not finding any information about that on the uniprot page | 17:11 |
| delinquentme | kanzure, you havnt any experience interfacing rails applications with java do you? | 17:11 |
| Juul | delinquentme, i have a bit | 17:11 |
| delinquentme | Juul, got my phone call from LBL .. dont recall if i mentioned .. the guy was awesome | 17:11 |
| delinquentme | no shit! | 17:11 |
| Juul | yeah you did :) hope you get it | 17:12 |
| delinquentme | So I've just finished this JRuby interface and Ive got a few ideas about getting it to interface | 17:12 |
| delinquentme | SOAP API ( w a separate server ), Tomcat servlet or jruby on rails | 17:12 |
| delinquentme | what did your implementation look like? | 17:13 |
| Juul | i played a bit with jruby, but decided to go with plain ruby and call rjb for java calls | 17:13 |
| Juul | so i'm running vanilla rails with rjb for interfacing to java and rsruby for interfacing to R | 17:14 |
| Juul | i try to stay away from the java world as much as i can | 17:14 |
| Juul | it's all so heavy | 17:14 |
| Juul | brb phone | 17:14 |
| delinquentme | yeah java is a biggun | 17:17 |
| kanzure | anything that uses soap is a waste of your time | 17:17 |
| delinquentme | Juul, do you happen to have a code sample of that interface? | 17:18 |
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| Juul | delinquentme, yeah, let me get it for you | 18:00 |
| Juul | delinquentme, here http://pastebin.com/2jTy86Nj | 18:02 |
| delinquentme | danke | 18:03 |
| Juul | tomcat/glassfish is pain if you ask me | 18:05 |
| delinquentme | you've used em? | 18:12 |
| Juul | yes | 18:13 |
| Juul | it's been a few years since i used tomcat | 18:16 |
| Juul | we're still using glassfish for some legacy code | 18:16 |
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| delinquentme | its really wild that they use tools like that | 18:19 |
| delinquentme | I guess I'd expect nothing but pure java .. like the fact ruby is mentioned at all is really wild to me | 18:19 |
| Juul | who? | 18:21 |
| Juul | the sad fact is that java is slow | 18:21 |
| Juul | a lot of the time having something in 1/10th of the time is better than having something industrial grade | 18:22 |
| Juul | not slow in execution, just slow for developing complex web apps | 18:22 |
| Juul | Hibernate is a monster | 18:22 |
| Juul | ActiveRecord is nicencess | 18:23 |
| Juul | delinquentme, how's the pay at that job? | 18:27 |
| delinquentme | no idea | 18:30 |
| delinquentme | hoping its not 50k | 18:30 |
| delinquentme | Juul, howd you get into rails | 18:30 |
| delinquentme | and do you plan to stay out in SV? | 18:30 |
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| kanzure | cell mouse culture thing? http://www.ebay.com/itm/ws/eBayISAPI.dll?ViewItem&item=230735944396 | 19:14 |
| kanzure | erm | 19:14 |
| kanzure | *mouse cell culture thing | 19:14 |
| kanzure | "one-time-use mammalian cell culture system" is what phil goetz called it | 19:14 |
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| kanzure | this is a weird synthesizer | 19:39 |
| kanzure | http://www.alibaba.com/product-free/109600291/OligoMaker.html | 19:39 |
| kanzure | about $120 | 19:39 |
| kanzure | "The OligoMaker 48/6 is a fast cost-effective 48-channel oligonucleotide synthesizer. The Six base bottle positions, can be upgraded to 8 or 10 or more bottle position. The OligoMaker 48/6 can be upgraded to make 96 or 192 oligos in parallel." | 19:39 |
| kanzure | http://www.oligomaker.com/ | 19:41 |
| kanzure | "OligoMaker ApS was founded back in 1996 as a technology R&D division of TAG Copenhagen A/S. OligoMaker ApS is located in the Symbion Science Park in Copenhagen in the center of the area known as The Medicon Valley." | 19:41 |
| kanzure | maarrrc | 19:42 |
| delinquentme | lerrrnin programming lernninnnn programmerang | 19:43 |
| kanzure | "OligoMaker is a fast cost-effective oligonucleotide synthesizer | 19:43 |
| kanzure | OligoMaker can synthesize ex. 10 oligos (20-mer) in less than 2.5 hours | 19:43 |
| kanzure | OligoMaker can be upgraded to make 96 or 192 oligos in parallel" | 19:43 |
| delinquentme | oh kanzure you'd know this Rjb::load(classpath = jars , jvmargs=[]) | 19:43 |
| kanzure | hm? | 19:43 |
| delinquentme | if im after the value of classpath ... thats me looking within the Rjb class for the classpath object right | 19:43 |
| kanzure | um, what? | 19:44 |
| kanzure | are you asking if your rjb instance has a classpath variable? | 19:44 |
| delinquentme | looking for 1) how to check the values within that classpath var | 19:45 |
| delinquentme | and confirmation that im using the correct nomenclature | 19:45 |
| bkero | http://coreyshields.com/images/bkero.png | 19:46 |
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| kanzure | bkero: attach it to your ceiling and then we will talk, sir | 19:46 |
| kanzure | delinquentme: i don't know, is it in your current namespace or not | 19:46 |
| kanzure | oligomaker video: http://www.youtube.com/watch?v=hBbjfEj1lCc | 19:47 |
| bkero | kanzure: impossible, I had to hold those damn cards up with yogurt containers and a proc box! | 19:48 |
| kanzure | http://www.labbase.net/Supply/SupplyItems-1098780.html | 19:52 |
| kanzure | "call for quote"... | 19:52 |
| kanzure | so i bet that meant $50,000 euro not $50.000 euro | 19:52 |
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| kanzure | hi yashgaroth | 20:49 |
| yashgaroth | hey | 20:49 |
| delinquentme | ^^^^^^^^^^^^^^^^^^^^^^^^^ | 20:55 |
| yashgaroth | ^ | 20:56 |
| kanzure | yashgaroth: i am having a brain fart | 20:57 |
| yashgaroth | oh my | 20:57 |
| kanzure | i'm pretty sure someone has done oligo ligation for gene assembly | 20:57 |
| kanzure | am i making this shit up? | 20:57 |
| yashgaroth | no, it's pretty standard for anything over 100 bp | 20:58 |
| kanzure | yeah but i mean, from an oligo library | 20:58 |
| kanzure | not from 100 bp-synthesized-strands | 20:58 |
| yashgaroth | oh, then I don't think so no | 20:58 |
| kanzure | that sounds stupid | 20:58 |
| yashgaroth | not like the 6mer thing, but I don't keep up much on gene synthesis as long as it gets delivered | 20:58 |
| kanzure | i've def. seen stuff like "LOL we synthesized 50 bp fragments of this GENE and REASSEMBLED IT!" | 20:58 |
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| yashgaroth | at a certain point, dealing with the 99% accuracy means cloning out your fragments, confirming them, and then ligating | 20:59 |
| yashgaroth | but it's not the basic technique like we'd be doing | 20:59 |
| kanzure | so i'm trying to be cautious against a potential argument that SU will give me: | 21:00 |
| kanzure | "you claim oligo mail order companies will go the way of the dinosaur, but why won't they just use a ligation scheme" | 21:00 |
| kanzure | *ligation scheme + oligo library | 21:00 |
| yashgaroth | oh btw U.S. patent scheme is going first-to-file in 3 weeks, rather than first-to-invest like it was previously | 21:01 |
| kanzure | *invent | 21:01 |
| yashgaroth | yes | 21:01 |
| yashgaroth | they totally could do it if it works, I mean they do already have the oligo synthesis infrastructure | 21:01 |
| yashgaroth | although -invest is pretty accurate as well considering you have to demonstrate it works first, which means $ | 21:02 |
| yashgaroth | please excuse my errors as I've been out getting drunk this evening | 21:02 |
| yashgaroth | so are we going with the oligo library assembly, or is all this speculation about modifying pol going to happen | 21:04 |
| kanzure | oligo library | 21:04 |
| kanzure | that google group thing is for the speculation about polymerase ;) | 21:04 |
| yashgaroth | oh thank god, all this talk about modifying pol to selectively add nucleotides is way in the future | 21:05 |
| kanzure | yes | 21:05 |
| kanzure | i want to write a roadmap with that googlegroup | 21:05 |
| kanzure | i think it would be cool to attach our names to it | 21:05 |
| kanzure | it can basically be "Here's a bunch of shit we've thought about, and some 3d models and simulation results" or something | 21:05 |
| yashgaroth | okay good, cuz I was worried we'd spend 10 years trying to get pol to work how we want | 21:06 |
| kanzure | nope. but! i would very much like it to be us who comes up with that method | 21:06 |
| yashgaroth | I think we could, no one's out commercially with something like that | 21:07 |
| kanzure | no researchers either | 21:07 |
| yashgaroth | I think we could test out the ligation scheme fairly easily, the 4096-droplet microfluidics is beyond my comprehension though | 21:08 |
| kanzure | okay, new scenario | 21:08 |
| kanzure | let's say the synthesis companies are somehow (magically) able to sell for $0.00001/bp | 21:08 |
| yashgaroth | mm | 21:08 |
| kanzure | so a full genome costs maybe $20 | 21:08 |
| kanzure | would an at-home synthesizer still win? | 21:09 |
| yashgaroth | oh man that's so far beyond my...I can't even imagine what a $20 genome sequencing would do, much less a synthesis | 21:09 |
| kanzure | yeah, synthesis | 21:10 |
| kanzure | with the polymerase you can even imagine it costing $0.00000000001/bp (let's say it eats atmospheric nutrients, bitches) | 21:10 |
| yashgaroth | well of course at that point the commercial synth would win, but there's no way they're getting 0.0000001/bp any time soon with pamidites | 21:10 |
| yashgaroth | oh, with an engineered pol it's maybe possible | 21:11 |
| kanzure | why would a commercial service win though | 21:11 |
| yashgaroth | oh, are we assuming both are the same price or what | 21:11 |
| kanzure | sure | 21:11 |
| kanzure | yes same price | 21:11 |
| kanzure | or, let's say this: | 21:11 |
| yashgaroth | then there's always the delivery time | 21:11 |
| kanzure | commercial is $0.0001/bp | 21:11 |
| kanzure | at home is $5k down, but $0.000001/bp | 21:11 |
| yashgaroth | I don't know how many biohackers we expect to have, but for any lab the 5k is nothing | 21:12 |
| yashgaroth | academic/commercial lab, but 5k for endy's suitcase is still cheap | 21:12 |
| yashgaroth | still, the only way to begin comparing cost per bp is to try it out | 21:13 |
| kanzure | "thats the value I see.... put the system on 'engineer mode' and when the bell rings, I've got a freshly evolved morphine operon" | 21:14 |
| yashgaroth | "? | 21:14 |
| kanzure | just a quote from nate | 21:14 |
| kanzure | so, delivery time | 21:15 |
| yashgaroth | and for the massively-parallel panning stuff, which'll be a much bigger user | 21:15 |
| kanzure | yeah for sure | 21:15 |
| yashgaroth | 'oh we have a sequence, let's try 10,000 variations of it tomorrow, sequencer go!' | 21:15 |
| kanzure | but currently the market doesn't buy that much massively-parallel dna synthesis | 21:15 |
| kanzure | right | 21:16 |
| kanzure | i mean, that's what i would use it for :) | 21:16 |
| yashgaroth | the panning market's perfectly willing to adopt that for affinity maturation | 21:16 |
| kanzure | affinity binding? | 21:16 |
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| nmz787 | hola | 21:16 |
| nmz787 | como estas | 21:16 |
| kanzure | in this channel we speak ENGLISH | 21:17 |
| yashgaroth | yeah, you have a clone, let's say you want to try every possible permutation of the loop | 21:17 |
| nmz787 | yo quero DIY hplus | 21:17 |
| yashgaroth | si | 21:17 |
| yashgaroth | see if you get better binding/expression, and repeat 'til you have a drug | 21:17 |
| kanzure | so, delivery time & parallel reactions -- | 21:17 |
| kanzure | you can't get them to ship you 1 million test tubes | 21:17 |
| kanzure | but you can make 1 million permutations by ligating things together differently | 21:17 |
| yashgaroth | exactly | 21:18 |
| kanzure | well, they probably could ship you 1 million test tubes | 21:18 |
| kanzure | in giant boxes | 21:18 |
| kanzure | but the costs of that would be.. tremendous | 21:18 |
| yashgaroth | still, oligo assembly could already be better than traditional synthesis | 21:19 |
| yashgaroth | only one way to find out | 21:19 |
| kanzure | yeah i'm sure it is better | 21:19 |
| kanzure | and if it is, those companies can just switch to it | 21:19 |
| yashgaroth | not if you patent the shit outta that bitch | 21:19 |
| yashgaroth | not that that's very DIY, but you gotta get that seed money | 21:20 |
| yashgaroth | I'd say it's 'non-obvious' since it took me a minute to type it out, but I'm no lawyer | 21:21 |
| kanzure | nah there's lots of patentable stuff here | 21:21 |
| kanzure | unfortunately this means i have to kill all of yuou | 21:21 |
| yashgaroth | I'm well armed | 21:21 |
| nmz787 | i know people that are well armed | 21:21 |
| kanzure | hey someone just posted to diybio | 21:22 |
| kanzure | named "brian doom" | 21:22 |
| kanzure | doom is an awesome name | 21:22 |
| yashgaroth | even twin eh? it happens | 21:22 |
| kanzure | evil? | 21:22 |
| yashgaroth | heh | 21:22 |
| kanzure | how drunk are you | 21:23 |
| kanzure | because you're still sorta able to think | 21:23 |
| yashgaroth | unless you have a mustache, he's the evil one by default | 21:23 |
| kanzure | you need to go drink mroe | 21:23 |
| yashgaroth | I'm still coherent but im having a hard tiem tryping this stuff without am=sabjf | 21:23 |
| kanzure | drink until my code makes sense http://diyhpl.us/~bryan/sciencedirect/sciencedirect.js | 21:24 |
| nmz787 | http://www.ncbi.nlm.nih.gov/pubmed/7590320 | 21:24 |
| yashgaroth | does not rely on DNA ligase but instead relies on DNA polymerase to build increasingly longer DNA fragments during the assembly process HA wait lemme read it | 21:24 |
| nmz787 | i have access | 21:25 |
| nmz787 | if you dont | 21:25 |
| yashgaroth | that's still long oligos specifically made for that gene | 21:25 |
| kanzure | 40nt means they probably had hybridizing overlaps | 21:25 |
| yashgaroth | I have no access to anything :( | 21:25 |
| kanzure | yes | 21:25 |
| kanzure | that's not an oligo libraryt | 21:25 |
| kanzure | that's "HEY we know what we want to synthesize" | 21:26 |
| nmz787 | sortof is | 21:26 |
| nmz787 | right | 21:26 |
| kanzure | it's 56 members of a 40mer library | 21:26 |
| kanzure | 56 / (4^40) is.... basically 0 | 21:26 |
| yashgaroth | sideways 8 | 21:26 |
| yashgaroth | err for 4^40 that is | 21:26 |
| kanzure | yashgaroth: you suck at unicode ∞ | 21:27 |
| yashgaroth | FUCK | 21:27 |
| yashgaroth | ∞ copy n pasting like a pro | 21:27 |
| nmz787 | but it says .9kb | 21:28 |
| nmz787 | 56*40 =2200 ish | 21:28 |
| nmz787 | 28*40=1120 | 21:28 |
| nmz787 | so even if the oligos had 20bp overlap per side, its longer than .9kb | 21:28 |
| kanzure | yeah some parts are for overlap | 21:28 |
| kanzure | hrm | 21:29 |
| nmz787 | and if that was the case, they wouldnt need poly | 21:29 |
| yashgaroth | well, a 3-5 mer overlap would be enough, as long as they stick at a temperature where pol still works | 21:29 |
| nmz787 | of they say 1.1kb was synthesized | 21:30 |
| nmz787 | oh* | 21:30 |
| yashgaroth | kanzure re: your js code, I'm far past the ballmer point sorry | 21:32 |
| nmz787 | so we need to just try this in an eppendorf | 21:33 |
| yashgaroth | indeed, just a 200bp fragment as proof of concept | 21:34 |
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| yashgaroth | I can supply the ep tubes :V | 21:38 |
| kanzure | ParahSailin: yo | 21:38 |
| kanzure | would you be willing to do some monkey labor | 21:38 |
| ParahSailin | monkey labor? | 21:38 |
| ParahSailin | sounds like fun | 21:38 |
| kanzure | you know.. lab monkeying | 21:38 |
| ParahSailin | what you have in mind at this point? | 21:39 |
| kanzure | nmz787: just ligase right? | 21:39 |
| yashgaroth | if we're doing a single-strand extension, we don't need PNK etc | 21:40 |
| nmz787 | http://disinfo.s3.amazonaws.com/wp-content/uploads/2011/09/MonkeysAtTypewriters.jpg | 21:41 |
| nmz787 | we'd need it for the staircase method or whatever you called it | 21:42 |
| yashgaroth | but if the bottom strand just guides the top one into position for the ligase, and then you wash it off | 21:42 |
| nmz787 | single stranded extension will not have polymerization control | 21:42 |
| yashgaroth | ^and repeat | 21:43 |
| nmz787 | monkeys at typewriters today, monkeys with pipettes tomorrow | 21:43 |
| yashgaroth | a brave new future, a monkey could do most of my job | 21:43 |
| ParahSailin | i think the "staircase method" would probably end up making a nice smear | 21:44 |
| yashgaroth | as long as he doesn't try to fuck my 50mL tubes I'll hire one | 21:44 |
| yashgaroth | okay back on topic, re smear you mean a lot of incorrect strands or what | 21:44 |
| kanzure | contaminants? | 21:45 |
| ParahSailin | random nastiness in general | 21:45 |
| nmz787 | why do you think that? | 21:45 |
| yashgaroth | the hope is that at least 5-10% will be correct | 21:45 |
| ParahSailin | i dunno, thats just my intuition/molecular bio pessimism | 21:45 |
| nmz787 | with the PNK and BAP for polymerization controls... | 21:45 |
| nmz787 | 5-10%!!!! | 21:46 |
| nmz787 | i was thinking it would be >90% | 21:46 |
| yashgaroth | pick 20 colonies til you get a good one, no problem | 21:46 |
| yashgaroth | depends how long the strand you're trying to make is | 21:46 |
| kanzure | 200bp | 21:47 |
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| yashgaroth | considering that for straight up pamidite, 69bp is a 50% success rate | 21:47 |
| ParahSailin | what we need is a 1000-10000bp one step synthesis | 21:48 |
| ParahSailin | up to 200bp, pamidite is good | 21:48 |
| yashgaroth | yeah I'm hoping we can do 1kbp, but 200 as a proof-of-concept | 21:48 |
| ParahSailin | gotcha | 21:48 |
| kanzure | ParahSailin: http://diyhpl.us/~bryan/papers2/DNA/enzymaticSynthesisCycle.png | 21:49 |
| kanzure | nmz787: where's the new diagram :x | 21:49 |
| nmz787 | errr | 21:49 |
| nmz787 | umm | 21:49 |
| nmz787 | shit | 21:49 |
| kanzure | hah | 21:49 |
| nmz787 | i got busy | 21:49 |
| nmz787 | next week is finals week | 21:49 |
| kanzure | sounds lame | 21:49 |
| nmz787 | i'm totally lethargic | 21:49 |
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| kanzure | Juul: http://oligomaker.com/ | 21:50 |
| nmz787 | the stress of hating school has gridlocked my neural circuitry | 21:50 |
| kanzure | Juul: do we have anyone in diybio who can go raid their facilities? they are in copenhagen | 21:50 |
| Juul | wut | 21:50 |
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| klafka | LOL | 21:50 |
| kanzure | on aliabbi this machine is being sold for $60 euro | 21:50 |
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| kanzure | *alibaba | 21:51 |
| kanzure | nmz787 suspects that it's a typo and it's supposed to be $60,000 euro | 21:51 |
| Juul | what the hell is that machine? | 21:51 |
| yashgaroth | I can hit them while I'm over there in vacation, get me jason statham and it'll be no problem | 21:51 |
| kanzure | Juul: 196-channel oligo sythesizer | 21:51 |
| Juul | that website looks like crap | 21:51 |
| Juul | they're just reselling? | 21:51 |
| kanzure | web design by http://www.simpelside.dk/ | 21:51 |
| kanzure | alibaba has someone reselling | 21:52 |
| kanzure | oligomaker is the manufacturer | 21:52 |
| kanzure | "Simpel Side leverer billige hjemmesider med CMS og høj fleksibilitet på | 21:52 |
| kanzure | få dage. Du kan vælge mellem 4 skabeloner og altid selv redigere i | 21:52 |
| kanzure | indholdet på din hjemmeside når som helst. " | 21:52 |
| kanzure | something something about 4 templates | 21:52 |
| Juul | so the manufacturer is in denmark | 21:52 |
| kanzure | i can't read this language too well | 21:52 |
| Juul | "Simple Page delivers cheap homepages with CMS and high flexibility in only a few days. You can choose between 4 templates and always edit the content of your website at any time" | 21:53 |
| kanzure | lame | 21:53 |
| Juul | yes it actually says "always at any time" | 21:53 |
| kanzure | hehe | 21:53 |
| kanzure | videos! | 21:54 |
| kanzure | http://www.youtube.com/watch?v=hBbjfEj1lCc | 21:54 |
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| Juul | so you want one of their machines? | 21:54 |
| nmz787 | i guess i'm heading to bed | 21:54 |
| kanzure | Juul: possibly, depending on the price | 21:54 |
| kanzure | i'm trying to igure out if this is actually $60 euro | 21:54 |
| kanzure | or $60,000 euro | 21:54 |
| nmz787 | it is not $60 euro | 21:54 |
| kanzure | will you eat your hat if it is | 21:54 |
| nmz787 | most of the parts on their parts page are =>$60 | 21:54 |
| nmz787 | umm | 21:55 |
| nmz787 | ugh | 21:55 |
| Juul | kanzure, i could ask them if they have some old broken stuff they're willing to donate to BiologiGaragen | 21:55 |
| nmz787 | what do i get if i eat my hat? | 21:55 |
| kanzure | Juul: that would be awesome | 21:55 |
| nmz787 | its wool | 21:55 |
| nmz787 | i don't think thats healthy to eay | 21:55 |
| Juul | kanzure, ok that's on my todo for tomorrow | 21:55 |
| nmz787 | http://news.bbc.co.uk/2/hi/health/425609.stm | 21:56 |
| nmz787 | ttyl | 21:56 |
| nmz787 | i will try to add the missing steps to the diagram tomorrow | 21:56 |
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| Juul | i was offered a job at upcoming Stanford BIOFAB today | 21:57 |
| Juul | but it will only be two people until more funding is found :-/ | 21:57 |
| kanzure | would this job possibly pay you? | 21:57 |
| kanzure | in money? | 21:57 |
| kanzure | hmm it looks like there's a video about the team that made the POSAM dna synthesizer | 21:58 |
| kanzure | http://youtube.com/watch?v=Nb7zxKEZzZQ | 21:58 |
| kanzure | maybe this is a different group.. | 21:58 |
| kanzure | that was a really lame video | 22:01 |
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| Juul | yes, it would pay me in money | 22:15 |
| Juul | but i would have to live near stanford or commute | 22:15 |
| Juul | and it would be more time out of my life not working on my own projects | 22:16 |
| Juul | this is sub-optimal | 22:16 |
| kanzure | right | 22:16 |
| Juul | also, i'm worried that it will take a while before we get funding for more people | 22:17 |
| kanzure | hasn't biofab been around for a few years now? | 22:17 |
| kanzure | how does it not have funding | 22:17 |
| Juul | two years yeah | 22:18 |
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| Juul | though the work is good and important, no articles have come out. also: the people involved all have other priorities | 22:18 |
| Juul | also, academia in the u.s. is apparently hella slytherin | 22:19 |
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| Juul | a couple of articles are on their way out | 22:19 |
| Juul | but it has taken crazy long, in part due to too many people being involved | 22:19 |
| klafka | slytherin? | 22:20 |
| kanzure | is it just me or does a lot of biofab/ginkgo/igem stuff seem to be pretentious a bit | 22:20 |
| Juul | hm, i couldn't say. the problem at biofab has been that there are two overworked professors in charge and they're both trying to act as managers/editors, and they have to agree | 22:21 |
| Juul | on what a good paper looks like | 22:21 |
| Juul | klafka, harry potter reference. from wikipedia: "Slytherin house values ambition, cunning, leadership, and resourcefulness. The house mascot of Slytherin is the serpent," | 22:22 |
| klafka | aaah | 22:23 |
| Juul | lots of maneuvering and strategizing. a lack of transparency in dealings and plans | 22:23 |
| klafka | ooh yes | 22:23 |
| klafka | fucking yes | 22:23 |
| yashgaroth | i.e. 'fuck you I'm first author' | 22:23 |
| klafka | oh so fucking yes | 22:23 |
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| klafka | man i can't sleep so i'm trying to figure out zendesk's rest api | 22:24 |
| klafka | ugh | 22:24 |
| kanzure | is it actually restful | 22:24 |
| klafka | not for me | 22:24 |
| klafka | (har har har) | 22:24 |
| Juul | its always problematic to have many people collaborating on editing one document, especially when everyone else has other priorities and it's almost impossible to get everyone to sit down and talk at the same time | 22:24 |
| delinquentme | anyone know where I could get more chemical formulas?? | 22:25 |
| kanzure | delinquentme: pubchem | 22:25 |
| delinquentme | just asked in ##chemistry | 22:25 |
| klafka | kanzure i think so | 22:25 |
| klafka | also what would make it not restful? COMET? | 22:25 |
| kanzure | delinquentme: pubchem > ##chemistry | 22:25 |
| kanzure | klafka: not restful means it's not using POST, GET, PUT, etc. | 22:25 |
| klafka | oh | 22:25 |
| klafka | ok | 22:25 |
| delinquentme | y no RESTful? | 22:25 |
| kanzure | and the objects wouldnn't be resources and shit | 22:26 |
| klafka | why would someone call a non-restful api restful then | 22:26 |
| klafka | :( | 22:26 |
| delinquentme | REST = Representational state transfer ... its related to POST GET DELETE etc | 22:26 |
| * klafka nods | 22:26 | |
| delinquentme | klafka, because they're not programmers | 22:26 |
| klafka | ah | 22:26 |
| delinquentme | and they want a brandname | 22:26 |
| delinquentme | call it restful = street cred | 22:27 |
| delinquentme | REST is basically HATEOS which is basically discoverability | 22:27 |
| delinquentme | ( correct me if im wrong ) | 22:27 |
| delinquentme | Juul, Rjb is awesome just got it working | 22:27 |
| delinquentme | kanzure, what should i put in here | 22:28 |
| delinquentme | just any kind of chemical and get a match | 22:28 |
| kanzure | sure | 22:28 |
| delinquentme | "water" << too simple | 22:29 |
| kanzure | do an alcohol | 22:29 |
| delinquentme | but these are pre-parsed | 22:30 |
| delinquentme | i want the human journal descriptions | 22:30 |
| yashgaroth | hexenal :D | 22:31 |
| Juul | delinquentme, cool | 22:31 |
| ParahSailin | wonder if any of the nad+ using ligases could be made electrochemically switchable | 22:32 |
| Juul | has anyone answered the question: "why has no biological organism evolved radio communication" | 22:35 |
| Juul | it seems like a natural progression from the electro-sensing and electro-communication found in some sea-creatures | 22:36 |
| klafka | that's not really an answerable question | 22:36 |
| klafka | all you can make is a convincing 'just-so story' | 22:36 |
| Juul | well you can come up with a reasonable hypothesis | 22:36 |
| klafka | fair enough | 22:36 |
| Juul | i'm wondering what the difficult component is | 22:37 |
| Juul | the oscillator? | 22:37 |
| Juul | the antenna? | 22:37 |
| yashgaroth | the solid metal antenna | 22:37 |
| Juul | possibly | 22:37 |
| Juul | would it have to be solid metal | 22:37 |
| Juul | ? | 22:37 |
| yashgaroth | dunno, I'm not an electronicizer | 22:38 |
| yashgaroth | I can't think of any emission/reception of spectra that are outside of the sun's normal wavelengths, much less all the way into radio | 22:39 |
| Juul | since it's much easier to communicate with simple electro-senses under water, but much harder / impossible to use radio, it might be that the jump between electro-sense and radio never happened, since it would have to happen in an amphibious species | 22:40 |
| Juul | well, it's pretty great that the radio spectrum isn't flooded by animal communication | 22:41 |
| yashgaroth | are there any examples of electro-communication underwater? I thought it was all prey detection | 22:41 |
| Juul | that would have both sucked for us and for the animals when we started disrupting their communication globally | 22:41 |
| Juul | yashgaroth, I believe I found some sharks that use it for communication last time i checked. let me see if i can find it again | 22:42 |
| yashgaroth | I'd thought it was platypus detecting prey, and electric eels doing their thing, but I've never looked into it much | 22:43 |
| delinquentme | Juul, umm ? @ the radio communication | 22:43 |
| delinquentme | we have they're called sound waves and simply on a shorter wavelength? | 22:43 |
| kanzure | there's some magnetoreceptor proteins | 22:43 |
| delinquentme | and dogs hear in a greater range so you could make an argument that they do | 22:43 |
| Juul | https://en.wikipedia.org/wiki/Electroreception#Electrocommunication | 22:43 |
| yashgaroth | ya for compass-like stuff in birds and bacteria | 22:44 |
| kanzure | Juul: a scifi story about us disrupting electromagnetic animal communication would be pretty neat | 22:44 |
| delinquentme | amulae of lorezini :D | 22:44 |
| Juul | kanzure, good idea. that's actually a good idea for how to spread the ideas you don't intend to / have time to implement | 22:45 |
| ParahSailin | an organism could probably make an antenna out of a well-conducting melanin | 22:48 |
| yashgaroth | oh man that radiation-eating fungus was so awesome | 22:48 |
| yashgaroth | melanin as chloropyll aww yeah | 22:49 |
| yashgaroth | +h* | 22:49 |
| kanzure | sshh the radiation-eating fungus was classified | 22:50 |
| yashgaroth | damn russkies | 22:50 |
| Juul | delinquentme, yeah sound waves are nice for comms, but the first animal to evolve radio would be able to communicate without detection by all other species | 22:54 |
| Juul | then everyone else would have to evolve radio to keep up | 22:54 |
| Juul | and eventually it would be no advantage whatsoever | 22:55 |
| Juul | and everyone would revert back to regular noisemakers as they require less energy | 22:55 |
| ParahSailin | the reason organisms dont have stuff for radio waves is that a microwave photon of 2.4 GHz has energy of .2 cal/mol | 22:55 |
| Juul | omg dinosaurs totally had telepathic walkie-talkie | 22:55 |
| Juul | <-- drunk | 22:55 |
| ParahSailin | atp = 7ish kcal/mol | 22:56 |
| delinquentme | Juul, i dont hear bats :D | 22:56 |
| delinquentme | $ bundle install_the_dependencies_stupid_gem_manager | 22:57 |
| ParahSailin | i dont think there's anything else in nature that can integrate such small quanta | 22:57 |
| kanzure | good night | 22:57 |
| Juul | huh? what does cal/mol mean for a photon? | 22:57 |
| Juul | kanzure, night | 22:57 |
| delinquentme | oodles kanzure | 22:57 |
| delinquentme | Juul, well its a source of energy right? | 22:58 |
| delinquentme | a cal / mol is a measure of energy capacity | 22:58 |
| ParahSailin | kcal/mol is the common biochemical unit of energy | 22:58 |
| ParahSailin | 1.5e-24 J = .0002 kcal/mol | 22:58 |
| foucist | ParahSailin: PariahSalin would make more sense wouldn't it? :P | 22:58 |
| * delinquentme thinks of the orange-hot headers of a car | 22:58 | |
| delinquentme | energy = heat, sound, light | 22:58 |
| * delinquentme sinatra installed | 22:59 | |
| Juul | per mole? why per mole? | 22:59 |
| Juul | 1 calorie is 4.184 joules | 23:00 |
| Juul | i'm not sure where the /mol comes in | 23:00 |
| ParahSailin | if you multiply a scalar by 6.022e23 it becomes a mol | 23:00 |
| Juul | oh. i've only seen that used when talking about something per number of atoms/molecules | 23:01 |
| Juul | didn't realize it was used as a general unit | 23:01 |
| Juul | you make a good point | 23:02 |
| ParahSailin | the si unit of light flux involves moles | 23:02 |
| yashgaroth | it's useful when comparing the energy of single molecule reactions | 23:02 |
| Juul | interesting | 23:02 |
| Juul | ok | 23:02 |
| Juul | i have to pack up and head for bart | 23:02 |
| ParahSailin | maybe not on the si unit | 23:03 |
| Juul | ParahSailin, so your argument is that reception wouldn't work? | 23:04 |
| Mokstar_AFK | hey | 23:04 |
| ParahSailin | reception would be pretty difficult to evolve id say | 23:04 |
| Mokstar_AFK | can microwave radiation convert l-proline into d-proline? | 23:04 |
| ParahSailin | lots of it can | 23:04 |
| Juul | hrm | 23:04 |
| Juul | ok | 23:04 |
| Juul | yep | 23:05 |
| ParahSailin | we havent seen biological heat engines either for that matter | 23:05 |
| Juul | what's the cal/mol of a light photon | 23:05 |
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| yashgaroth | I thought the general rule was that a receptor has to be at least half the length of the wavelength it's receiving, which for radio is hella long | 23:05 |
| ParahSailin | or biological mechanical force to atp transducers | 23:05 |
| ParahSailin | chlorophyll a blue peak 465 nm photon is 2.666 eV | 23:07 |
| ParahSailin | 1 eV = 23 kcal/mol | 23:08 |
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| ParahSailin | stuff like heat engines and radio receptors just dont scale down that well i guess | 23:10 |
| ParahSailin | to the molecular level i mean | 23:10 |
| delinquentme | ParahSailin, you know of the ssingle molecule sterling engine right? | 23:11 |
| ParahSailin | hadnt heard of it, but that seems to be micron scale | 23:13 |
| ParahSailin | also, kinda cheating to use optical tweezers as the pistons :) | 23:15 |
| ParahSailin | big difference between Angstrom scale protein supramolecular assemblies and microparticles | 23:16 |
| ParahSailin | a sarcomere in muscle is a 2 um supermolecular assembly | 23:17 |
| ParahSailin | but myosin motors individually work at the angstrom level | 23:17 |
| ParahSailin | so its evolutionarily feasible | 23:17 |
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