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| nmz787 | kanzure: I tried bumping the quality of an example of this and got a stack size limit error from recursion http://openjscad.org/ | 01:08 |
|---|---|---|
| nmz787 | too bad too, because they have a lot of API and their docs seem really really good | 01:09 |
| nmz787 | this is a demo where your code changes will update | 01:10 |
| nmz787 | http://joostn.github.io/OpenJsCad/ | 01:10 |
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| kanzure | "Bacteriophage adhering to mucus provide a non–host-derived immunity" http://www.pnas.org/content/110/26/10771.short | 07:05 |
| kanzure | "Based on these observations, we present the bacteriophage adherence to mucus model that provides a ubiquitous, but non–host-derived, immunity applicable to mucosal surfaces. The model suggests that metazoan mucosal surfaces and phage coevolve to maintain phage adherence. This benefits the metazoan host by limiting mucosal bacteria, and benefits the phage through more frequent interactions with bacterial hosts. The relationships shown ... | 07:05 |
| kanzure | ... here suggest a symbiotic relationship between phage and metazoan hosts that provides a previously unrecognized antimicrobial defense that actively protects mucosal surfaces." | 07:05 |
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| kanzure | -_- marcus hutter http://consc.net/pics/singularity@@/aixi.jpg | 07:14 |
| kanzure | er... this is a strange email | 07:15 |
| kanzure | it's from "Herschel Shmuel Pinchas Yerucham Krustofsky <herschelshmuelpinchasyerucham@gmail.com> | 07:15 |
| kanzure | er, -" | 07:16 |
| kanzure | sent to diybio-israel@googlegroups.com | 07:16 |
| kanzure | "I have another good friend looking for a shidduch. His name is Alfred Rosenberg and he is in his early 30's. He is a modern yeshivish guy from New York who is now living in Bnei Brak. He is a brilliant biochemist hired by the Mossad to develop an ethnic bioweapon to eliminate Arabs, liberals, and mothers-in-law. Mr. Rosenberg is open to dating women from all backgrounds or walks of life, including divorcees and converts, even older ... | 07:16 |
| kanzure | ... women up to age 40 If you know any young women in the parshah whom you think might be appropriate for him, please give him a call at 054-550-7796 or call me at 074-701-0411. " | 07:16 |
| kanzure | very odd troll | 07:16 |
| kanzure | "The Mossad, short for HaMossad leModiʿin uleTafkidim Meyuḥadim, is the national intelligence agency of Israel." | 07:17 |
| kanzure | huh, this spam seems to be everywhere | 07:17 |
| archels | haha, what in the hell. | 07:22 |
| archels | have you tried calling the numbers? | 07:22 |
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| kanzure | no | 07:28 |
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| heath | https://github.com/indrora/Atomic | 07:37 |
| heath | Atomic: an IRC client from the ashes of yaaic | 07:37 |
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| maaku | happy new year everyone | 08:16 |
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| kanzure | no time travel | 08:19 |
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| bbrittain | maaku: you too! | 08:31 |
| maaku | well it's 2015 where I am :P | 08:31 |
| bbrittain | kanzure: he is a time traveler. *gasp* | 08:32 |
| kanzure | time travel is very dangerous | 08:32 |
| bbrittain | maaku: asia? | 08:33 |
| maaku | bbrittain: taipei | 08:34 |
| maaku | kanzure: I wish there was a sci fi movie that really, properly investigated time travel in a serious way | 08:35 |
| bbrittain | I love taipei. | 08:35 |
| maaku | Primer probably comes the closest | 08:35 |
| maaku | bbrittain: who wouldn't? taipei has everything | 08:35 |
| bbrittain | 台北是我的最喜欢的城市 | 08:36 |
| kanzure | there was a study recently where someone crawled the web looking for evidence of time travel | 08:36 |
| bbrittain | and about 100x more 7/11s than you need | 08:36 |
| kanzure | if i was better at conspiracy theories, i would spin some lies about how the web is really just a CERN project related to particle acceleration and time travel | 08:36 |
| maaku | lies? | 08:37 |
| maaku | :P | 08:37 |
| bbrittain | maaku: do you live in taipei or just traveling? | 08:38 |
| kanzure | everyone knows that the only way that time travelers are able to communicate is through crazy usenet emails from the 80s | 08:38 |
| kanzure | because CERN was hosting a usenet node back then | 08:38 |
| kanzure | next to their synchotron | 08:38 |
| kanzure | maaku: have you been exposed to the "molecular biology and cells are already self-replicating nanotechnology and we should be using that instead of employing fantasies of diamondoid mechanosynthesis" line of reasoning before? | 08:40 |
| maaku | bbrittain: eh.. both? my wife is from taipei city. we're on extended travel / remote work at the moment, staying with her aunt downtown (nearest MRT Chiang Kai‑shek Memorial Hall) | 08:41 |
| maaku | i'll be back stateside in a few weeks though. gotta make fc15 in peurto rico in late january | 08:42 |
| bbrittain | maaku: very nice. I imagine it's quite nice out there. Every time I've been there there has been a typhoon :/ | 08:42 |
| bbrittain | kanzure: is that a bad line of logic? | 08:42 |
| bbrittain | that makes perfect sense to me... | 08:42 |
| maaku | haha i've yet to experience one of those. we usually don't go during typhoon season | 08:42 |
| maaku | feels like summer in san fransico | 08:42 |
| maaku | kanzure: it's a great idea if what you want to do is biology | 08:44 |
| kanzure | bbrittain: well the most reasonable objection that i've seen is "biology sucks and the protocols suck and it's not anything like engineering" | 08:44 |
| maaku | meh who cares if it's not like engineering, so long as it gets the job done | 08:44 |
| kanzure | maaku: hm? you can do lots of non-biology sttuff with biology. like you can make proteins to do... things.. and structured like.. things. | 08:44 |
| maaku | but from what i can tell it doesn't get the job done | 08:44 |
| kanzure | wait, which job in this context pls? | 08:45 |
| bbrittain | biology? correct. | 08:45 |
| bbrittain | :P | 08:45 |
| maaku | kanzure: curing all diseases, ending aging, strengthening the body against mechanical failure, mind uploading. in that order. | 08:47 |
| bbrittain | maaku: those are some hefty jobs | 08:48 |
| bbrittain | I vaugly expect it to be easier in this order: strengthening body, ending aging, curing all diseases, mind uploading. | 08:49 |
| kanzure | "curing all diseases" should be dead last | 08:49 |
| bbrittain | well if we have mind uploading, would it be worth it to even cure all diseases? | 08:49 |
| kanzure | i would be pretty happy with "a general ability and good reasons to expect anyone to be able to cure biological disease" rather than "some sort of centralized attempt at disease erradication" | 08:50 |
| kanzure | well anyway, hm | 08:52 |
| kanzure | actually, i might place mind uploading as easier than ending aging | 08:52 |
| bbrittain | kanzure: I think thats crazy, the brain is obscenly complicated | 08:54 |
| bbrittain | maaku: are you saying you think that biology, just doesn't get the job done? | 08:55 |
| bbrittain | IIRC, you worked at transcriptic; did that influence that opinion? | 08:55 |
| kanzure | generally i think it's probably correct to say things like "it is harder to do those things with biology than it would be with generic molecular nanotechnology" | 08:55 |
| maaku | sorry was afk | 08:56 |
| maaku | bbrittain: no, transcript is awesome and does good work | 08:56 |
| bbrittain | good to hear, they are seeming more and more useful | 08:57 |
| kanzure | maaku: i don't know if i have indoctrinated you into the cult of diybio yet, but the lab centralization trends are worrisome | 08:57 |
| kanzure | on the one han, i think a generic biology lab api is a good thing | 08:57 |
| kanzure | on the other hand, it's already hard enough for me to acquire good lab equipment | 08:57 |
| maaku | the ordering of those tasks has to do with singularity related concerns, somewhat unrelated (i maybe shouldn't have specified order) | 08:58 |
| kanzure | centralization would tend to make acquiring equipment even more difficult | 08:58 |
| maaku | but taking them in the order listed... | 08:58 |
| maaku | cure all diseases: we have diseases for which we know the mechanism, or we know how to identify affected cells (e.g. cancers). yet these diseases remain uncured | 09:00 |
| maaku | this is embarassing. the problem is that the tools available to us from biology don't provide the necessary functionality to destroy the disease | 09:00 |
| maaku | we should be able to e.g. scan the genome of every cell for certain virus dna, and remove if found + carry out some other procedures, or identify cancerous cells or viruses or bacteria and destroy in place | 09:01 |
| kanzure | cancer is not a good example because of the million different mechanisms | 09:02 |
| kanzure | certain subtypes of cancer are excellent examples, though | 09:02 |
| maaku | kanzure: no it's a perfect example because there are specific cancers which we can identify (you do a biopsy and say "these cells are cancer of type XYZ"), and yet you still die of the damn disease | 09:03 |
| kanzure | we do have ways to destroy certain types of cancers based on personalized medicine (e.g. custom viruses) but again this does not work for all forms of cancer | 09:03 |
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| bbrittain | I tend to agree that that is embarassing though | 09:04 |
| maaku | why can't we? oh yeah, biology is basically doing chemistry with boxing gloves (protiens), applied shotgun style to the body. even personalized medicine fits this category | 09:04 |
| bbrittain | maaku: oh, I don't think thats quite fair | 09:06 |
| bbrittain | shotgun, yes | 09:06 |
| bbrittain | but that can be refined | 09:06 |
| bbrittain | "personalized medicine" is a joke right now | 09:06 |
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| maaku | i'm not saying its useless. I'm just saying it'd be so much better if we could remove the gloves | 09:07 |
| bbrittain | the proteins? elaborate. | 09:08 |
| maaku | no just metaphorically. having the ability to e.g. destructively disassemble a cell, recording the exact composition, structure, and position of every molecule found within | 09:10 |
| maaku | or the ability to selectively inject a protien, rna, or other package into any specific cell | 09:11 |
| maaku | or the ability to "map-reduce" operations on the body -- identify cells by arbitrary constraint X, perform arbitrary operation Y | 09:12 |
| maaku | that would go pretty damn far towards curing all diseases | 09:12 |
| maaku | and is the sort of thing provided by Freitas-like nanomedecine built with diamandoid tools, not biology | 09:13 |
| maaku | similarly for biology -- if you can do atomically precise studies on representative cell types and tissue from a very large population, identifying the causes of ageing is basically an exericise in statistical analysis | 09:14 |
| maaku | 3rd item, i would like to upgrade the human body such that it is able to disperse the energy of an high energy bullet, survive catestrophic breakup of an airliner, survive without oxygen for 24 hours, and probably a host of other things requried to make sure accidental death no longer occurs | 09:16 |
| maaku | for curing disease, ending ageing, and radical body upgrades, wet biology doesn't seem to cut it for the above mentioned reasons. and I have yet to hear of a way to achieve mind uploading via biology only | 09:18 |
| bbrittain | haven't you seen avatar? (I'll have more serious responses onec I'm done making this coffee) | 09:19 |
| maaku | so kanzure, I respect the people who say that we should improve on biotech rather than diamandoid nanotechnology. they are often solving real problems today and for that deserve my respect. | 09:21 |
| maaku | but i do claim they're not dreaming big enough :) | 09:21 |
| fenn | fwiw drexler takes the position we should work on biotech first | 09:21 |
| maaku | fenn: I think that is a misrepresentation. drexler is working on bootstrapping diamandoid mechanosythesis via engineered protien structures | 09:23 |
| kanzure | that sounds like biotech to me | 09:23 |
| maaku | kanzure: maybe. another way of looking at it is traditional engineering, just using DNA as scaffolds, lipids as container walls, etc. the structures I've seen very clearly look engineered | 09:24 |
| fenn | we also build houses out of wood :\ | 09:26 |
| fenn | http://metamodern.com/2009/03/19/a-high-performance-polymer-for-nanosytems-engineering/ | 09:28 |
| kanzure | in the absence of working molecular nanotechnology, biotech seems like a good way to get stuff done | 09:30 |
| maaku | kanzure: right, well my response is "sounds like someone needs to be working on molecular nanotechnology!" | 09:30 |
| fenn | "to my astonishment the field has languished on the sidelines, and often isn’t thought of as being a nanotechnology." | 09:31 |
| maaku | i'm okay with working on long-term, high-payoff projects. indeed i tend to gavitate towards those | 09:31 |
| fenn | [the field of rational protein design] | 09:31 |
| bbrittain | I think that none of these are mutually incompatable. Ideally we would reach a point in biotech where iff a diamonoid mechanism works better, it could just be incorporated, no? | 09:32 |
| bbrittain | My bigest problem with biotech is how every single thing just increases complexity, not decreases it. :/ | 09:33 |
| fenn | no, not if your technology is completely modular and resuable components, as biology tends to do | 09:33 |
| fenn | vs covalent one-off structures made of pure carbon or whatever | 09:34 |
| bbrittain | fenn: sorry, did you just say that biology is completely modular?! | 09:34 |
| fenn | yes | 09:34 |
| fenn | on a chemical level at least | 09:34 |
| maaku | fenn: right, but notice how he talks about joining peptide chains together into atomically precise configurations, laments the lack of CAD-like tools, and stresses the differences from biology (his words) | 09:35 |
| bbrittain | I mean, thats like saying a processor is modular because electricity. | 09:35 |
| maaku | he's talking about atomically precise ceramics, not meat | 09:35 |
| kanzure | he's talking about protein | 09:35 |
| fenn | ceramics is incorrect, but i agree | 09:35 |
| fenn | we don't have a word for this material probably | 09:36 |
| kanzure | the other day i viewed the images of all rcsb pdb proteins with more than 300 residues (tens of thousands of proteins) | 09:36 |
| maaku | Right sorry, that's obviously not correct. And yeah I don't konw what the word would be for that material... | 09:36 |
| kanzure | out of all of those, here are some with interesting and novel shapes http://diyhpl.us/wiki/dna/projects/#proteins | 09:37 |
| kanzure | however, there's a few hundred thousand proteins with less than 300 residues | 09:37 |
| fenn | .c 300^20 | 09:37 |
| yoleaux | 300²⁰ = 34867844010000000000000000000000000000000000000000 | 09:37 |
| fenn | or is it 20^300 | 09:37 |
| bbrittain | .c 20^300 | 09:38 |
| yoleaux | 20³⁰⁰ = 2037035976334486086268445688409378161051468393665936250636140449354381299763336706183397376000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 ≈ 2.037035976334486 | 09:38 |
| bbrittain | :D | 09:38 |
| kanzure | also the the enzymatic therapy article on wikipedia is pretty hilarious ("just inject the enzymes straight into the blood what's the worst that can happen") | 09:39 |
| maaku | bbrittain: yes you could replace something bio with something diamandoid. but that's missing the point that diamandoid tools cannot ever exist in the bio world | 09:40 |
| bbrittain | anyways, maaku I would like to see more engineering in biology. I think that biology can be used in ending aging/curing diseases. helpful/core to strengthening body. and not useful to mind uploading, at least in any form we currently recognize as biology | 09:40 |
| kanzure | there are definitely ways to use biology to help with mind uploading | 09:40 |
| kanzure | like antibody tagging | 09:40 |
| fenn | or protozoa threading fiberoptics through the brain | 09:42 |
| kanzure | or expression of certain signals | 09:42 |
| kanzure | and the glorious technique of in utero electroporation | 09:43 |
| kanzure | i wonder if anyone has done radioisotope tracing of mouse learning, e.g. inject radioisotopes straight into blood, train the critter on some task, "sacrifice" four hours later, examine incorporation of radioisotopes into molecular structures | 09:45 |
| kanzure | ah right, one of the claims is that existing structures may be sufficient without incorporation of matter for long-term storage, nevermind | 09:46 |
| fenn | that gets you fMRI data at best | 09:47 |
| kanzure | "“Something I’d like to do, which I think many of our engineers will be hearing this in real-time, is have the charge connector plug itself in. Like an articulating, like sort of a snake, like Metal Gear Solid or something.”" - my bro elon | 09:47 |
| kanzure | nah, once you sacrifice the critter you can scan brain slices and look more closely | 09:47 |
| maaku | bbrittain: I don't see them as contradictory paths. what I hope to see accomplished with molecular nanotechnology is the creation of tools that help medical professionals cure diseases | 09:48 |
| superkuh | paperbot: http://www.nature.com/nmat/journal/vaop/ncurrent/full/nmat4164.html | 09:49 |
| paperbot | http://libgen.org/scimag/get.php?doi=10.1038%2Fnmat4164 | 09:49 |
| kanzure | .title http://www.nature.com/nmat/journal/vaop/ncurrent/full/nmat4164.html | 09:49 |
| yoleaux | Soft 3D acoustic metamaterial with negative index : Nature Materials : Nature Publishing Group | 09:49 |
| superkuh | Thinking lenses for ultrasonic brain stimulation. | 09:49 |
| fenn | aka flubber | 09:49 |
| superkuh | Up to 500 KHz in that paper. | 09:50 |
| maaku | the tension comes from the fact that atomically precise nanotechnology is a revolutionary advancement, not evolutionary. | 09:51 |
| maaku | from the biologist's perspective, the nanotechnologists provide nothing useful for 15 - 20 years, until their "nanofactory" is finished and suddenly massive new capabilities are possible | 09:52 |
| kanzure | superkuh: so you would do single-use metamaterials for specific stimulation/regional dosages? take off metamaterial and switch to a different cap for another round of differently-located stimulation? | 09:53 |
| superkuh | I'm still trying to figure out what Mie resonators are, but yeah, something like that. | 09:55 |
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| kanzure | nmz787: another option is you could try python-brlad | 11:01 |
| kanzure | er | 11:01 |
| kanzure | python-brlcad | 11:01 |
| nmz787 | diybio israel, huh... never heard of that before.... that spam sounds exactly appropriate for that list though, oddly | 11:01 |
| kanzure | that spam is elsewhere on the internet, it's just a bot | 11:01 |
| nmz787 | dear spambot, the FBI is now watching you | 11:02 |
| nmz787 | fuck, if the FBI connects us with spambots | 11:02 |
| nmz787 | 'there are clearly maligned intentions in the eastern diybio community, bring biocurious to the ground bos' | 11:02 |
| nmz787 | boys* | 11:03 |
| nmz787 | kanzure: I thought there was tons of stuff missing from brl-cad | 11:03 |
| nmz787 | or python-brlcad | 11:03 |
| nmz787 | so bluetooth 4.0 (BLE) is supported on Android 4.3+ and also iOS with app-store authentication (as opposed to pre BLE requiring a hardware ID chip on your custom hardware) | 11:05 |
| * nmz787 designed some BLE system stuff the last few days for automotive trailer lights testing from a phone | 11:05 | |
| nmz787 | it's too bad the $15 rfduino didn't have 16 pins instead of only 8 (since I didn't want to deal with muxers), I ended up going with an nRF8001 and arduino mini | 11:07 |
| kanzure | .wik rfduino | 11:28 |
| yoleaux | kanzure: Sorry, I couldn't find article. | 11:28 |
| kanzure | .wik bladerf | 11:29 |
| yoleaux | "This article provides a list of commercially available software-defined radio receivers." — http://en.wikipedia.org/wiki/List_of_software-defined_radios | 11:29 |
| bbrittain | bladerf is cool | 11:42 |
| bbrittain | I have a myraidrf coming | 11:42 |
| bbrittain | kanzure: you are obsessed with ribosomes, right? | 11:52 |
| eudoxia | ah i see from the logs that kanzure has given up on mechanosynthesis | 12:00 |
| eudoxia | well that's a shame i guess i gotta grow up now too | 12:00 |
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| kanzure | eudoxia: i never say i gave up | 12:41 |
| kanzure | eudoxia: that's not fair | 12:41 |
| kanzure | bbrittain: no, i think it would be more fair to say i am obsessed with polymerases http://diyhpl.us/~bryan/papers2/polymerase/ | 12:42 |
| bbrittain | "I lost this page once with a crash in Opera" | 12:43 |
| bbrittain | found your problem | 12:43 |
| bbrittain | Opera | 12:43 |
| kanzure | 400 tabs | 12:43 |
| bbrittain | nah, just Opera | 12:43 |
| kanzure | none of the other browsers can really do that these days | 12:43 |
| kanzure | even with my 32 GB of RAM | 12:44 |
| bbrittain | well, have you considered you may have a tab problem? | 12:44 |
| kanzure | yes, i decided i don't | 12:44 |
| kanzure | the main reason why i like polymerase is because of the idea of direct control over its enzymatic synthesis of dna | 12:46 |
| kanzure | or rna, i don't really care | 12:46 |
| kanzure | bbrittain: http://diyhpl.us/~bryan/papers2/polymerase/roadmap.pdf | 12:46 |
| eudoxia | well that's terse | 12:47 |
| kanzure | "we're working on it" | 12:47 |
| kanzure | "not much progress, guys" | 12:48 |
| kanzure | hmm i should remember to write stuff in there | 12:49 |
| kanzure | there were a handful of good ideas sent to the mailing list | 12:51 |
| kanzure | so they just need to be written up in a document form | 12:51 |
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| kragen | BLE is sounding increasingly awesome | 13:12 |
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| -!- Topic for ##hplusroadmap: biohacking, nootropics, transhumanism, open hardware | sponsored by george church and the NRA, banned by the Federal Death Administration (4 times) | this channel is LOGGED: http://gnusha.org/logs | http://diyhpl.us/wiki | 14:35 | |
| -!- Topic set by kanzure [~kanzure@unaffiliated/kanzure] [Sat Dec 27 16:56:22 2014] | 14:35 | |
| [Users ##hplusroadmap] | 14:35 | |
| [ altersid_] [ cluckj ] [ dvorkbjel] [ kragen ] [ Qfwfq ] [ superkuh ] | 14:35 | |
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| -!- Irssi: ##hplusroadmap: Total of 69 nicks [0 ops, 0 halfops, 0 voices, 69 normal] | 14:35 | |
| -!- Channel ##hplusroadmap created Thu Feb 25 23:40:30 2010 | 14:35 | |
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| kanzure | hi EnabrinTain | 14:56 |
| delinquentme | kanzure, opinion: | 15:02 |
| delinquentme | found a quiet fail in a codebase submitted by a googler ... was first to find it + report | 15:03 |
| delinquentme | worth mentioning ? | 15:03 |
| kanzure | er, why not report it? | 15:03 |
| delinquentme | already did | 15:05 |
| delinquentme | should I throw that in as a bullet point on the resume? | 15:05 |
| delinquentme | perhaps I need a bugs reported section of the resume | 15:05 |
| kanzure | oh, well i'd have to see your resume to know that | 15:05 |
| delinquentme | oh! you've not seen my resumes? | 15:07 |
| delinquentme | https://gist.github.com/carlcrott/4480bf5f522c178a4c22 | 15:07 |
| delinquentme | gist.github.com/carlcrott/9172903 | 15:07 |
| delinquentme | one is the white-washed version | 15:07 |
| kanzure | move your experience section to the top | 15:08 |
| kanzure | everything else is irrelevant | 15:08 |
| kanzure | you have at least 8 years of experience listed, you're an old fart at this point | 15:09 |
| delinquentme | and IDK if this dudes title is anything impressive: https://www.linkedin.com/in/erjohnso | 15:11 |
| delinquentme | also im pissed. im not a 1% er | 15:12 |
| delinquentme | im a 5%er | 15:12 |
| delinquentme | Oh and whats also awesome is 3drobotics is still after me :D | 15:14 |
| kanzure | maaybe keep your education section, but honestly nobody should care | 15:21 |
| * EnabrinTain waves at kanzure | 15:25 | |
| EnabrinTain | Happy Year Everyone | 15:26 |
| * juri_ waves. | 15:30 | |
| delinquentme | kanzure, always better to highlight best aspects | 15:42 |
| delinquentme | marketing is ehhhh | 15:42 |
| delinquentme | my projects speak way louder | 15:42 |
| delinquentme | https://github.com/apache/libcloud/commit/95ae5beea125797ba3bd07028af1dbbd65dc2265#commitcomment-9131116 | 15:43 |
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| delinquentme | kanzure, if we wanted to blow money for NYE | 15:56 |
| delinquentme | what would we be doing | 15:56 |
| kanzure | NYE? | 15:56 |
| delinquentme | you think so? | 16:05 |
| delinquentme | Ohh sorry. new years eve | 16:05 |
| delinquentme | tonight | 16:05 |
| delinquentme | sorry I thought you meant NYC | 16:05 |
| delinquentme | idk if thats our style | 16:05 |
| cluckj | booze is traditional | 16:26 |
| cluckj | tiny party hats for your cats is non-traditional | 16:29 |
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| kanzure | hm | 17:43 |
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| kanzure | gene_hacker: good pics on page 69 http://diyhpl.us/~bryan/papers2/neuro/Identification%20and%20functional%20analysis%20of%20Trnp1%20-%20a%20novel%20DNA%20associated%20protein%20with%20a%20key%20role%20in%20neurogenesis.pdf | 18:21 |
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| kanzure | HEx1: https://groups.google.com/d/msg/enzymaticsynthesis/3YEEv0OULo0/zJZPETWDbMIJ | 18:22 |
| kanzure | actually that link is prolly good for gene_hacker too | 18:23 |
| HEx1 | kanzure: yes, replying's been on my list of thing to do for several days now | 18:23 |
| HEx1 | +s | 18:23 |
| kanzure | ah | 18:23 |
| kanzure | so the system works! | 18:23 |
| kanzure | sort of | 18:23 |
| HEx1 | yeah, I just suck is all | 18:24 |
| kanzure | any other ideas bouncing around for dna/peptide synthesis? | 18:25 |
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| HEx1 | synopsis: maybe it would be an improvement over existing chemical peptide synthesis methods if you could add a dozen or so (up to 19 I guess) tRNAs in a single step. might get better yields that way | 18:26 |
| kanzure | oh, how would you choose which tRNA gets used though? | 18:26 |
| kanzure | oh, you mean some in-solution capping/decapping solution that can discriminate against ~20 different tRNAs..... hmm. | 18:27 |
| kanzure | i'm not sure we have any cappers that are that good | 18:27 |
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| HEx1 | not quite. have mRNA with each triplet once each, repeatedly. then have a buttload of tRNAs loaded with the aminos you actually want, then add lots of them simultaneously | 18:29 |
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| * HEx1 reads about decapping | 18:30 | |
| kanzure | oh, that is the proposal that cathal suggested in response in that thread | 18:30 |
| kanzure | i think | 18:30 |
| HEx1 | I thought he was proposing only two triplets, which alternate, and thus you only add one tRNA per step | 18:31 |
| kanzure | "one tRNA" you mean one molecule? | 18:33 |
| kanzure | i think you add millions of them, but all of the same type (same amino acid, same mRNA specificity) | 18:33 |
| HEx1 | no, one type | 18:33 |
| kanzure | right ok | 18:33 |
| kanzure | oh, you're right, if you have an alternating code in mRNA, then you could add two types of tRNA at a time | 18:33 |
| kanzure | because one will go first, and the other next | 18:34 |
| HEx1 | no you couldn't, because it wouldn't stop after two, you'd get an arbitrary amount of addition | 18:34 |
| HEx1 | if you had mRNA with, say, AAAGGGAAAGGG..., you'd add GGG-tRNA with the amino you wanted, wash, add AAA-tRNA with the amino you wanted second, wash, etc. | 18:35 |
| kanzure | oh sorry, you're right, i'm thinking of (n + 1) mRNA triplets, and then you can use n types of tRNA | 18:35 |
| HEx1 | exactly. we have 20 types of tRNA, we could add 19 at once. speedup: 19x. yield: potentially 19x, depends on ribosome efficiency (but they're pretty efficient, right?) | 18:36 |
| kanzure | (so that when the mRNA triplet pattern starts repeating, nothing gets added) | 18:36 |
| kanzure | i don't understand the 20 types thing you are suggesting | 18:37 |
| kanzure | you need to be sure that the correct amino acid gets added next | 18:37 |
| HEx1 | yes, you need mRNA that has each triplet in turn | 18:38 |
| kanzure | why though? maybe your protein doesn't need that next triplet | 18:38 |
| kanzure | the "pattern" is indicated by which tRNAs you add during each cycle | 18:38 |
| kanzure | and the mRNA is not custom (i mean, it's custom for this generic procedure, but not related to any particular future protein you will want to make) | 18:39 |
| kanzure | i seem to be alternating between understanding and not understanding :) | 18:39 |
| kanzure | based on my last message, that would mean my "n + 1" idea is wrong | 18:40 |
| HEx1 | the mapping between triplets and aminos is arbitrary. you need to be able to charge your tRNAs with whatever you want. if you can do that, and you have a complete set of 20*20=400 tRNAs then you can add 19 aminos in a single cycle by picking 19 tRNAs out of your library that match up with the 19 distinct triplets that come next in the mRNA | 18:40 |
| HEx1 | I should write a proper list reply explaining properly, when I'm actually sober | 18:41 |
| kanzure | oh right, any future protein you want to make can be coded because you have a tRNA for each mRNA triplet you know you will encounter... so "n + 1" does work. | 18:41 |
| kanzure | and you can even do "same amino acid at least n - 1 times in a row" | 18:42 |
| kanzure | right, well, are there any particular immediate applications to having the ability to print large proteins | 18:43 |
| HEx1 | unsure. when I was thinking about this a couple of years ago I concluded proteins were kind of a dead end. you can't bootstrap anything from them | 18:44 |
| kanzure | the number one constraint is coupling efficiency and yield on each nucleotide addition in dna synthesis | 18:45 |
| kanzure | and a similar constraint in chemical peptide synthesis | 18:45 |
| HEx1 | but the fact that chemical peptide synthesis is even a thing indicates that there is interest | 18:45 |
| kanzure | so even with gibson assembly you still encounter lots of yield issues | 18:45 |
| kanzure | chemical peptide synthesis has a max residue count of like 70 to 100 at the most | 18:46 |
| kanzure | (also things get built backwards, i dunno if this is a problem) | 18:46 |
| HEx1 | yeah. given that ribosomes can do 2 orders of magnitude better than that indicates that they're unlikely to be the limiting factor | 18:46 |
| HEx1 | interesting, hadn't run into Gibson assembly | 18:47 |
| delinquentme | I think. Im gonna go grab some junk food. and now that im no longer sleep depriveddddd | 18:47 |
| delinquentme | program! | 18:47 |
| kanzure | i wonder if there's any ribosome that is not made up of RNA | 18:49 |
| HEx1 | I was looking into existing cell-free expression systems to see what the current state is (obviously you couldn't do this in a cell) | 18:49 |
| kanzure | do those kits do anything new and exciting that they weren't doing years ago? | 18:50 |
| HEx1 | AIUI ribosomes are *ancient*, and highly conserved across all forms of life | 18:50 |
| HEx1 | I don't know what they were doing years ago, I'm a relative n00b at all this | 18:50 |
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| kanzure | if there was a protein-constructed ribosome then you could use ribosomes to print out better ribosomes | 18:52 |
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| HEx1 | but NEB's FAQ says "Synthetic tRNAs will have a hard time competing with the native tRNA pool." | 18:53 |
| kanzure | you could also bootstrap different dna polymerases that are hard to manually collect | 18:53 |
| kanzure | what native tRNA pool? | 18:53 |
| kanzure | native to my test tube ? | 18:53 |
| HEx1 | presumably the one that came in the kit along with the E.coli ribosomes | 18:54 |
| kanzure | ah | 18:54 |
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| kanzure | HEx1: another idea that i've seen recently is using enzymes in oligonucleotide synthesis and/or chemical peptide synthesis to increase coupling efficiencies and yields | 18:57 |
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| HEx1 | questions: how easy is it to make custom tRNA? how stable are membrane-bound ribosomes (and the growing proteins) after repeated wash cycles? | 19:12 |
| kanzure | both of these things are unknowns | 19:13 |
| kanzure | there have been synthetic tRNAs that incorporate unnatural amino acids | 19:13 |
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| HEx1 | theoretically tRNA is very easy to modify. the problem is that natural tRNA is also required for a cell to stay alive (modulo redundancy in the genetic code) | 19:17 |
| HEx1 | clearly I need to research what has been done so far | 19:18 |
| kanzure | oh, this would definitely not be in vivo | 19:18 |
| kanzure | although we could use cells to grow tRNAs :) | 19:19 |
| HEx1 | https://www.google.com/patents/US5358862 <-- hmm, people were playing with this long ago | 19:22 |
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| kanzure | "Synthetic tRNAs are produced from tRNACys (AAA), tRNASer (AAA), tRNAe Ala (AAA), and tRNAi Ala (AAA) genes. Polyuridylic acid-dependent syntheses of polypeptides were carried out in vitro on E. coli ribosomes using the synthetic tRNAs." | 19:25 |
| kanzure | nonribosomal peptide synthates could maybe synthesize genomes. but their sequences would be way larger than the entire genome (because you need like 8 amino acids per nucleotide you want to encode into the protein) | 19:29 |
| HEx1 | no. just no. | 19:30 |
| kanzure | haha | 19:31 |
| kanzure | i forget their name | 19:31 |
| kanzure | nonribosomal.. something.. | 19:31 |
| kanzure | "Nonribosomal peptides are synthesized by nonribosomal peptide synthetases, which, unlike the ribosomes, are independent of messenger RNA. Each nonribosomal peptide synthetase can synthesize only one type of peptide." | 19:33 |
| kanzure | nonribosomal peptide-synthetase (NRPS) enzymes" | 19:33 |
| HEx1 | like CCA-adding enzymes | 19:33 |
| kanzure | "The enzymes are organized in modules that are responsible for the introduction of one additional amino acid. Each module consists of several domains with defined functions, separated by short spacer regions of about 15 amino acids." | 19:33 |
| kanzure | "However the first fungal NRP to be found was ciclosporin. It is synthesized by a single 1.6MDa NRPS.[4] T" | 19:34 |
| kanzure | hm can't find that on pdb | 19:35 |
| kanzure | oh i see, ciclosporin isn't the protein | 19:36 |
| HEx1 | yeah. most things that aren't made by ribosomes *can't* be made by ribosomes. I'm sure there is a reason for the few that can | 19:39 |
| kanzure | i believe there are some "nonribosomal peptide synthetases" that can, at the very least, incorporate amino acids, so i think it may be possible to find some that add nucleotides | 19:40 |
| kanzure | i don't know if CCA-adding enzyme counts as a nonribosomal peptide synthetase | 19:40 |
| kanzure | " | 19:40 |
| kanzure | oh, my quote key didn't work both times. so no +" needed. | 19:40 |
| HEx1 | meh, categorisation doesn't matter, it is what it is | 19:41 |
| HEx1 | anyway. we should talk more when I have swapped this in a bit. meanwhile I need sleep | 19:43 |
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| delinquentme | guhhhhh | 19:58 |
| delinquentme | that server build | 19:58 |
| delinquentme | walking away for 5 mins | 19:58 |
| delinquentme | so goo | 19:58 |
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| kanzure | .title http://nar.oxfordjournals.org/content/19/20/5749.abstract | 20:22 |
| yoleaux | A synthetic alanyl-initiator tRNA with initiator tRNA properties as determined by flourescence measurements: comparison to a synthetic alanyl-elongator tRNA | 20:22 |
| kanzure | "Two synthetic tRNAs have been generated that can be enzymatically aminoacylated with alanine and have AAA anticodons to recognize a poly(U) template. One of the tRNAs (tRNAe Ala/AAA) is nearly identical to Escherichia coli elongator tRNAAla. The other has a sequence similar to Escherichia coli initiator tRNAMet (tRNAjAla/AAA). Although both tRNAs can be used in poly(U)-directed nonenzymatic initiation at 15 mM Mg2+ , only the elongator ... | 20:23 |
| kanzure | ... tRNA can serve for peptide elongation and polyalanine synthesis. Only the initiator tRNA can be bound to 30S ribosomal subunits or 70S ribosomes in the presence of initiation factor 2 (IF-2) and low Mg2+ suggesting that it can function in enzymatic peptide initiation." | 20:23 |
| kanzure | .title http://link.springer.com/protocol/10.1385%2F0-89603-397-X%3A105 | 20:23 |
| yoleaux | In Vitro Engineering Using Synthetic tRNAs with Altered Anticodons Including Four-Nucleotide Anticodons - Springer | 20:23 |
| kanzure | "Synthetic tRNAs—those that are transcribed in vitro from a DNA sequence that has been ligated into an appropriate plasmid—have a wide variety of applications that range from testing tRNAs for their requirements for amino-acylation (1) to providing reagents for the investigation of protein folding (2). The examples that will be described here involve specific tRNAs with altered anticodons. The construction of several of these tRNAs ... | 20:24 |
| kanzure | ... will be given in detail as examples of the procedure applied. Also, methods of use and how to test the efficiency of these tRNAs will be reviewed." | 20:24 |
| kanzure | related: "Exploring the limits of codon and anticodon size | 20:24 |
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| -!- poohbear is now known as poohyear | 20:27 | |
| kanzure | .title http://pubs.acs.org/doi/abs/10.1021/ja025872a | 20:37 |
| yoleaux | An Error Occurred Setting Your User Cookie | 20:37 |
| kanzure | "We report herein a new method for the aminoacylation of tRNA, using a resin-immobilized ribozyme and the cyanomethyl ester (CME) of an amino acid substrate. The oxidized form of the ribozyme was immobilized on a hydrazine resin via covalent linkage. We performed aminoacylation of tRNAs using this ribozyme-resin to isolate aminoacyl-tRNAs. The column was recycled up to 5 times without significant activity loss. Thus, our ribozyme-based ... | 20:37 |
| kanzure | ... aminoacylation system has significant potential to be a powerful and practical technique for supplying various nonnatural aminoacyl-tRNAs for a highly efficient in vitro translation system." | 20:37 |
| kanzure | "Aminoacyl-tRNA Synthesis by a Resin-Immobilized Ribozyme" | 20:37 |
| kanzure | oh man i completely forgot about flexizyme stuff | 20:40 |
| fenn | heh anderson cooper doesn't understand comedy at all | 20:47 |
| kanzure | are they still irradiating your eyeballs geeze | 20:48 |
| fenn | this was self inflicted... enablers | 20:48 |
| fenn | i like to watch the new york countdown | 20:49 |
| kanzure | https://www.youtube.com/watch?v=bPBzj90Su8A | 20:49 |
| fenn | .title | 20:49 |
| yoleaux | Quark They Irradiated Their Own Planet? - YouTube | 20:49 |
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| fenn | why does he say it three times? | 20:51 |
| kanzure | youtube has this reality distortion field called "poop" | 20:51 |
| fenn | and it will destroy the universe | 20:51 |
| fenn | and has destroyed the universe | 20:51 |
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| kanzure | poop example https://www.youtube.com/watch?v=Bt7MN8f4YGk | 20:52 |
| delinquentme_ | https://www.youtube.com/watch?v=8xHXx5HARC8 fun.0 | 20:53 |
| kanzure | .title | 20:53 |
| yoleaux | 5 Crazy Science Stunts, You Won't See At School - YouTube | 20:53 |
| kanzure | meh | 20:54 |
| delinquentme_ | watch the second one | 20:58 |
| delinquentme_ | need liquid nitrogen | 20:58 |
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| fenn | man this place is totally dead quiet.. no explosions no nothing | 21:03 |
| kanzure | .title https://www.youtube.com/watch?v=UkEuIlGLZkY | 21:08 |
| yoleaux | Darth Vader sings the Internationale - YouTube | 21:08 |
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| gene_hacker | no explosions? then make them | 21:24 |
| delinquentme_ | omg | 21:30 |
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| delinquentme_ | also knights of sidonia is nuuuts as is gargantia on the vardious planet | 21:51 |
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| fenn | there's nothing like an alien/clone/hermaphrodite love triangle to warm the cockles of my heart | 22:08 |
| kanzure | this is a wonderful resource http://www.psydb.net/samples/original.php | 22:17 |
| fenn | .title | 22:18 |
| yoleaux | PsyDB: Psychedelic trance / psytrance samples: Original | 22:18 |
| fenn | is this where DJs get all the cheesy sound effects | 22:18 |
| kanzure | basically it's a reverse index of "weird quotes and samples you may have once heard many years ago in some random song while coding" | 22:18 |
| kanzure | for example, | 22:18 |
| kanzure | https://www.youtube.com/watch?v=g1LwIrAABVk | 22:19 |
| fenn | right | 22:19 |
| fenn | "the distance between insanity and genius is measured only by success" | 22:19 |
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| kanzure | https://www.youtube.com/watch?v=PZL8cjCzSPs&t=4m5s | 22:24 |
| nmz787 | .title | 22:27 |
| yoleaux | Cyclics - Movement Within the 4th Dimension - YouTube | 22:27 |
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| kanzure | ugh https://www.youtube.com/watch?v=W0ADdohktbQ&t=6m55s | 22:27 |
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| kanzure | too bad this index is incomplete. | 22:28 |
| fenn | http://fennetic.net/irc/orbital_moebius.mp3 | 22:28 |
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| kanzure | there's this one that i can't find that literally used quotes sampled from the back to the future movies | 22:32 |
| kanzure | usually i am pretty good at finding impossible to find things | 22:33 |
| kanzure | but this is hard when people name their tracks stuff like "DJ x volume 5140" | 22:33 |
| nmz787 | kanzure: wasn't there some other online CAD thing that had some non-free services associated? | 22:33 |
| kanzure | there are many online cad things | 22:33 |
| nmz787 | it was open though | 22:34 |
| nmz787 | I think | 22:34 |
| nmz787 | is that verb? | 22:34 |
| nmz787 | does it have some non-free front-end? | 22:34 |
| fenn | are you thinking netfabb? | 22:35 |
| delinquentme_ | waz told today that this is a pretty solid cad design package too: http://www.plm.automation.siemens.com/en_us/products/nx/for-design/ | 22:35 |
| kanzure | tinkercad upverter emachineshop shapesmith verbnurbs parametricparts floodeditor.com the list is really long don't make me think this hard | 22:35 |
| nmz787 | no I don't think it was netfabb, I don't remember seeing that | 22:36 |
| nmz787 | maybe floodeditor | 22:36 |
| kanzure | fenn: what's worse is that i have no way of knowing if it was scrobbled or not http://diyhpl.us/~bryan/irc/trance | 22:36 |
| nmz787 | which is down for me | 22:36 |
| nmz787 | 'like most cloud-based applications, your data is lost to you as long as the server is down' | 22:38 |
| kanzure | is that from the song? | 22:39 |
| fenn | .ety scrobble | 22:40 |
| yoleaux | Sorry, I couldn't find the etymology of that. | 22:40 |
| kanzure | the thing that dumps names of things into another thing while you are listening to some of those things | 22:40 |
| fenn | post-post-postmodern hangover trance | 22:40 |
| fenn | is "scrobble" a fancy word for "log" | 22:41 |
| kanzure | yes | 22:42 |
| fenn | i would like to do logging with mocp | 22:42 |
| nmz787 | hmm, I got something to work in verb with a nurbsSurface finally | 22:43 |
| fenn | i dont get the need for a connection to last.fm | 22:43 |
| nmz787 | so how is it that verb is able to 'render' nice looking things faster than implicitCAD? | 22:44 |
| kanzure | that's so they can monetize your data | 22:44 |
| nmz787 | or smoother rather | 22:44 |
| nmz787 | faster and smoother | 22:44 |
| kanzure | webgl magic | 22:44 |
| fenn | i dont want anyone monetizing my data | 22:46 |
| fenn | i just want the data | 22:46 |
| fenn | it seems lastfmsubmitd saves logs and uses logrotate at least | 22:46 |
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| nmz787 | damn, this looks really really cool http://portland.craigslist.org/clk/pho/4819884558.html | 23:24 |
| nmz787 | .title | 23:24 |
| yoleaux | Zeiss Interferometer / microscope | 23:24 |
| nmz787 | $1000 though | 23:25 |
| nmz787 | if the action is smooth though, that would be chump change for a stepper platform | 23:25 |
| nmz787 | unless it actually does .wik Classical interference microscopy | 23:29 |
| nmz787 | .wik Classical interference microscopy | 23:29 |
| yoleaux | "Classical interference microscopy (also referred to as quantitative interference microscopy) uses two separate light beams with much greater lateral separation than that used in phase contrast microscopy or in differential interference microscopy (DIC)." — http://en.wikipedia.org/wiki/Classical_interference_microscopy | 23:29 |
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