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| kanzure | darwin is making a cryonics facility | 05:35 |
|---|---|---|
| chris_99 | Mike Darwin? | 05:36 |
| kanzure | yes....? do we know other darwins? | 05:38 |
| chris_99 | is there any evidence that cryopreservation of humans may actually work? | 05:38 |
| kanzure | depends on what you mean by "works" | 05:45 |
| kanzure | so far we have not demonstrated cryoresuscitation of humans | 05:50 |
| kanzure | however, we have demonstrated cryoresuscitation of worms | 05:50 |
| kanzure | i think that there is a better chance of human cryopreservation and cryoresuscitation if we allow for gene therapy and genetic engineering to occur before vitrification and preservation | 05:53 |
| kanzure | .. and various selection projects... | 05:57 |
| kanzure | and as for thresholds for defining 'working', i think that 5% memory survival and only partial personality would still be tremendously useful. | 05:59 |
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| chris_99 | 5% seems very low doesn't it? | 06:20 |
| kanzure | compared to 0, i'd take it | 06:29 |
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| kanzure | __mz_o: the abi 391 pcr-mate manual is available here, http://diyhpl.us/~bryan/papers2/DNA/abi391/ | 06:49 |
| __mz_o | pssh thank you kanzure | 06:53 |
| __mz_o | been looking for that all morning | 06:53 |
| __mz_o | do you think its worth a purchase? | 06:53 |
| kanzure | the one i bought was <$500, if you're making lots of primers i guess that's okay | 06:55 |
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| __mz_o | the price is what had caught my attention | 07:15 |
| __mz_o | seemed too good to be true esp since its an old piece of equipment | 07:16 |
| __mz_o | im diving head first into this so i will have some questions later | 07:16 |
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| __mz_o | i know you can run custom cycles, could this synthesize peptides given the proper cycle/reagents? | 07:19 |
| kanzure | dunno. you should compare to the peptide synthesis machines instead. | 07:20 |
| kanzure | __mz_o: have you read http://diyhpl.us/wiki/dna/synthesis/notes/ | 07:20 |
| -!- darsie is now known as bad | 07:24 | |
| kanzure | which reminds me, i should ping CaptHindsight about this. he would be pretty happy about https://groups.google.com/d/msg/enzymaticsynthesis/uyZqtJO24RE/lApLb4JmCAAJ ... since it's compatible with inkjet dna synthesis. one of his fancypants 100 million drops/sec inkjet printheads would work perfectly with the assembly methods i outlined in that email. | 07:25 |
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| juri_ | sounds like fun. | 07:27 |
| yoleaux | 15 Nov 2016 14:14Z <__mz_o> juri_: were you ever able to render at .1? | 07:27 |
| kanzure | 07:25 < CaptHindsight> kanzure: I'll take a peek in a bit | 07:27 |
| juri_ | __mz_o: it's still rendering, at .5. it's taken long enough that i have a new lerease of ImplicitCAD, and a new server to run it on with more ram. | 07:28 |
| juri_ | this has been quite a challenge. thanks for starting me down this path. :) | 07:30 |
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| __mz_o | kanzure: thanks for pointing me to the synthesis notes. Makes understanding the manual a little better | 07:35 |
| __mz_o | I guess i have to scour and sift through the wiki sometime soon | 07:36 |
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| __mz_o | juri_: one would think that youre rendering the universe! lol | 07:36 |
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| CaptHindsight | kanzure: synthesizing genes for MRO (Maintenance, Repair and Operations) of organisms was my interest | 07:47 |
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| __mz_o | http://onlinelibrary.wiley.com/wol1/doi/10.1002/bip.22574/full | 07:48 |
| __mz_o | .title | 07:48 |
| yoleaux | Peptide and peptide nucleic acid syntheses using a DNA/RNA synthesizer - Pokharel - 2014 - Peptide Science - Wiley Online Library | 07:48 |
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| __mz_o | gotta find the full version somewhere | 07:49 |
| kanzure | CaptHindsight: gibson assembly can already put together entire genes, that's doable with modern techniques. | 07:50 |
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| CaptHindsight | kanzure: I was looking at something like 24 hour turn custom mods | 07:52 |
| kanzure | well, you would need virus manufacturing. the slow parts are DNA sequencing and validation of the synthesized fragments. | 07:53 |
| CaptHindsight | from blood or tissue sample to custom virus service | 07:54 |
| kanzure | a friend of mine is starting a synthetic virus company soon | 07:54 |
| kanzure | this is him https://lifeboat.com/blog/2016/11/synthetic-virus-created-to-treat-cancer-in-dogs | 07:54 |
| CaptHindsight | but after the last election I'm not sure about making it easily available | 07:55 |
| kanzure | nah, it will happen anyway. nature already creates tons of natural viruses every single day. we just need to get really, really good at virus defense projects. | 07:56 |
| __mz_o | you can always filter known undesirable sequences | 07:56 |
| kanzure | who is filtering? | 07:56 |
| __mz_o | and have an agreement to cya | 07:56 |
| kanzure | why would a "bad actor", running their own synthesizer, choose to filter the sequences they want...? | 07:56 |
| CaptHindsight | yeah why at least it would level the playing field | 07:56 |
| CaptHindsight | to have something inexpensive and fast | 07:57 |
| kanzure | yes. | 07:57 |
| kanzure | the alternative is "lol well we could potentially stop this virus, but it will cost $xyz millions" | 07:57 |
| kanzure | which is no good | 07:57 |
| kanzure | i have not looked into the actual equipment pipeline required for virus manufacturing | 07:58 |
| CaptHindsight | the tech seems to be scattered across several players and patents | 07:59 |
| juri_ | __mz_o: this will be the biggest render job completed by implicitcad. ;) | 08:00 |
| kanzure | my friend has a virus manufacturing facility that he has been testing, but it's not publicly documented (ugh) | 08:00 |
| __mz_o | he has/manages the lab or is just sending work to the lab? | 08:01 |
| kanzure | CaptHindsight: anyway the new detail i wanted to communicate to you is that, i think it's going to be possible to do "one pot" assembly of thousands of different DNA fragments into very long DNA fragments. right now we have gibson assembly and yeast homologous recombination which isn't good enough. but the feasibility of "one pot assembly" is really high. so after inkjeting, the process woul... | 08:02 |
| kanzure | ...d be "take all the constructed DNA fragments, and put it into a single reaction chamber, and run some other protocol [details pending at the moment]". | 08:02 |
| CaptHindsight | yeah I get it | 08:02 |
| kanzure | cool cool | 08:02 |
| CaptHindsight | CRISPR trials on humans has already started in China | 08:12 |
| CaptHindsight | University of Pennsylvania starts their trials next year | 08:13 |
| CaptHindsight | I wonder what they have planned for DNA synthesis at the Parker Institute for Cancer Immunotherapy? | 08:14 |
| kanzure | probably just outsourcing it | 08:15 |
| kanzure | nobody cares about synthesis :( | 08:15 |
| CaptHindsight | The National Cancer Institute (NCI) still outsources theirs | 08:15 |
| CaptHindsight | they are looking at finally doing it in house | 08:16 |
| CaptHindsight | a friend at the CDC didn't even want to hear about being able to make gene mods cheaply and quickly, it's just too scary | 08:22 |
| kanzure | well...... to me, what's scary is not having lots & lots of people trained to make immunological defenses to new viruses. we need lots of people thinking creatively about unique ways to defend biology against natural and unnatural biological threats-- we need new proteins, new cells, new systems. | 08:29 |
| CaptHindsight | ignorance or confidence that it's not needed yet? | 08:29 |
| kanzure | hm? | 08:30 |
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| CaptHindsight | or let things play out since the earth is overpopulated | 08:31 |
| CaptHindsight | and somehow those in power will still survive? | 08:32 |
| kanzure | ah you mean, why are they afraid. simple-- fearmongering is cheaper than positive forward moving progress. | 08:32 |
| CaptHindsight | yeah | 08:32 |
| kanzure | __mz_o: he owns the lab. or rather, he set it up. something like that. not outsourcing. | 08:36 |
| CaptHindsight | is there a secret underground bunker at the CDC that already has the defense tech? | 08:37 |
| kanzure | there's prolly some military stuff somewhere | 08:41 |
| kanzure | for defense of novel problems, i think you need human creativity and you still need to do the research... unlikely that there's single button defense solutions. | 08:42 |
| CaptHindsight | sounds like an opportunity | 08:46 |
| CaptHindsight | just needs some fake news to to generate interest | 08:46 |
| kanzure | "please panic because: government is hiding anti-virus tech from you"? | 08:47 |
| CaptHindsight | bad guys can make bad stuff, we need a quick defense system | 08:49 |
| CaptHindsight | duct tape won't save you this time | 08:51 |
| CaptHindsight | didn't save you last time either since only a few scary packages were publicized | 08:52 |
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| CaptHindsight | https://www.genomeweb.com/sequencing-technology/oxford-nanopore-releases-pricing-minion-flow-cells-users-publish-new-data | 09:21 |
| CaptHindsight | I surprised that there isn't a ChinaCo version of this yet | 09:22 |
| CaptHindsight | $500 per flow cell to $900 per flow cell | 09:22 |
| CaptHindsight | internal record was 1 gigabase per flow cell, and some users achieved more than 500 megabases per flow cell | 09:23 |
| CaptHindsight | Run time is not fixed, so output varies depending on the length of the run | 09:23 |
| CaptHindsight | some opportunity there for 2nd sources | 09:23 |
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| aedla | I wonder why the flow cells have a maximum yield.. Nanopores get damaged over time? | 09:42 |
| kanzure | maybe there are problems with sample prep | 09:44 |
| CaptHindsight | maybe they made theirs in a way that wears | 09:44 |
| CaptHindsight | look at the business model | 09:45 |
| CaptHindsight | this keeps the cash flowing with a consumable | 09:45 |
| CaptHindsight | now there is a patent battle between Oxford and illimina | 09:46 |
| CaptHindsight | http://www.bio-itworld.com/2016/2/24/illumina-sues-oxford-nanopore-technologies-over-composition-nanopores.html | 09:47 |
| CaptHindsight | why it wears https://nanoporetech.com/how-it-works | 09:48 |
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| aedla | the how-it-works page is interesting. I still don't get why it wears. although yeah, maybe just a business model | 10:25 |
| CaptHindsight | they appear to use a polymer membrane nanopore | 10:26 |
| CaptHindsight | ?-hemolysin is a heptameric protein pore with an inner diameter of 1 nm | 10:27 |
| CaptHindsight | not tough like SiO2 | 10:28 |
| CaptHindsight | or graphene | 10:29 |
| aedla | right.. and there's probably tons of stuff that can damage the protein pore over time, like radiation and oxygen? | 10:34 |
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| nmz787_w | sup | 11:25 |
| nmz787_w | I've not read logs in 1.5 weeks or so | 11:26 |
| nmz787_w | __mz_o: I don't think I took apart a PCR-mate... | 11:32 |
| nmz787_w | oh | 11:32 |
| nmz787_w | what a strange name for the synthesizer | 11:32 |
| nmz787_w | :/ | 11:32 |
| nmz787_w | I guess the marketed use was to make primers | 11:32 |
| nmz787_w | huh, the google image results for abi pcr mate are mostly from that take-apart | 11:33 |
| nmz787_w | folks should find some more stuff for me to take apart... I have a trailer and a garage and several LED shoplights that I can install on my garage ceiling for better photo illumination | 11:34 |
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| nmz787_w | __mz_o: worth buying depends on how committed to using it you are... I think I estimated a set of chemicals was something like $1300, including all the rinse solvents and stuff too | 11:35 |
| kanzure | plus they have expirations | 11:37 |
| kanzure | so usage means you have to prep everything to be shipped at the same time (roughly) | 11:38 |
| chris_99 | why do they expire out of interest, oxidation or something? | 11:41 |
| nmz787_w | yeah | 11:41 |
| nmz787_w | that and moisture | 11:41 |
| nmz787_w | which later provides an oxidizer for some reactions | 11:41 |
| chris_99 | hmm, theres no way to store them, in a way that stops that happening | 11:41 |
| chris_99 | like in nitrogen or something? | 11:41 |
| nmz787_w | the OH looks like the OH on the new monomers | 11:41 |
| nmz787_w | so it competes for polymer extension sites | 11:41 |
| nmz787_w | chris_99: yeah, expensive bottles with double septa, sureseal lids, nitrogen glove box for transfers | 11:42 |
| nmz787_w | lots of pain in the butt | 11:42 |
| chris_99 | ah heh | 11:42 |
| nmz787_w | I actually have a planned week+ off from work next month to devote to micro/nanofluidics tests | 11:43 |
| nmz787_w | figuring a few days to regroup my thoughts, few days to get software ready (which I can actually do in the coming weekends possibly), few days to spend in lab, few days to spend attempting to utilize what I made in lab | 11:43 |
| chris_99 | did you say you have a spin coater, i forget | 11:44 |
| nmz787_w | yeah | 11:44 |
| nmz787_w | so does the lab I am gonna use | 11:44 |
| chris_99 | cool | 11:45 |
| nmz787_w | they have the FIB, a spin coater, a plasma asher, carbon coater, gold coater, optical scopes with interference contrast | 11:45 |
| nmz787_w | chem fume hood | 11:45 |
| chris_99 | plasma asher? | 11:45 |
| nmz787_w | umm, probably other stuff | 11:45 |
| chris_99 | oh just wikipedia'd it, neat | 11:46 |
| nmz787_w | yeah it is a microwave oven which can adjust the power input in non-duty cycle PWM fashion (i.e. unlike a normal home microwave does... which is full on then full off) | 11:46 |
| nmz787_w | and you pull a slight vacuum | 11:46 |
| nmz787_w | maybe blow in some O2 if you care about other air gasses | 11:46 |
| chris_99 | is that remotely similar to plasma etching | 11:46 |
| nmz787_w | .title https://www.youtube.com/watch?v=N-R0_nXpc7I | 11:47 |
| yoleaux | Homemade Oxygen Plasma Etcher & PDMS to Glass Bonding Test - Black Box Labs - YouTube | 11:47 |
| nmz787_w | chris_99: yeah, it is a form | 11:47 |
| chris_99 | cheers, i'll watch that with sound later | 11:48 |
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| ybit | Farm Hack: worldwide community of farmers that build and modify our own tools https://news.ycombinator.com/item?id=13063541 | 13:04 |
| kanzure | http://gundam-challenge.com/ | 14:05 |
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| -!- bad is now known as darsie | 14:56 | |
| archels | .title http://medicalxpress.com/news/2016-11-clinical-trial-device-wounds-ultrasound.html | 15:27 |
| yoleaux | Clinical trial to test device that heals wounds with ultrasound | 15:27 |
| nmz787_w | http://farmhack.org/tools/rocket-clave-wood-fired-autoclave-0 | 15:27 |
| nmz787_w | "A 420lb propane tank is to serve as the sterilization chamber. " | 15:28 |
| nmz787_w | welp, the wording of this event feels pretty disclusionary http://nesawg.org/events/women-sustainable-agriculture-conference | 15:30 |
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| cluckj | no kidding? it's supposed to be | 15:42 |
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| nmz787_w | cluckj: idk about that... in the past I've contacted at least one or two events like this, mentioning how it seems to be discriminatory and going against company/university policy... and the response was always "oh no, men are totally allowed and encouraged" yet here I am still feeling like I'd be some huge asshole who'd get ostracized if I showed up at such events | 16:03 |
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| cluckj | you should go | 16:23 |
| cluckj | but like...just watch and listen | 16:24 |
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| kanzure | don't bring that in here | 17:02 |
| kanzure | got enough problems up in this joint | 17:02 |
| fenn | gundam global challenge seems to be unashamed about going for 100% entertainment value, instead of, you know, actually making a walking giant robot | 17:14 |
| fenn | ming-hsun chiang seems to be the only one trying to build a humanoid robot | 17:14 |
| fenn | well, the only accepted proposal | 17:15 |
| fenn | i bet all the japanese robotics professors are scared off by it being seen as too dorky to be affiliated with | 17:15 |
| kanzure | surely gundam has been around long enough that the robotics professors are all in the job because of the show | 17:23 |
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| kanzure | yashgaroth: greetings | 18:06 |
| kanzure | i am presently harassing juul about https://groups.google.com/d/msg/enzymaticsynthesis/uyZqtJO24RE/lApLb4JmCAAJ | 18:07 |
| yashgaroth | hoi | 18:07 |
| yashgaroth | oh yeah I should make a post there about the recombinase stuff | 18:10 |
| kanzure | eh just link to the logs, close enough | 18:13 |
| yashgaroth | true, wanna make the diagram with actual software rather than a pen and envelope tho | 18:14 |
| juul | kanzure: do i understand correctly that you're proposing a method of artificial selection that would require inserting a bunch of different 100 bps sequences into an organism, growing the organism, sequencing the organisms DNA on a per-cell basis and then keeping cells that manage to ligate the DNA, wash, rinse, repeat? | 18:14 |
| juul | or are you proposing that the 100 bp sequences are all designed such that only combining a bunch of them correctly will yield a viable selection marker? | 18:15 |
| fenn | thanks for the summary | 18:17 |
| juul | completely unrelated: I just discovered this journal https://www.alchemistowl.org/pocorgtfo/ | 18:21 |
| kanzure | juul: that's a good question. i'm not sure yet. i think that the selection marker approach doesn't work initially.... because homologous recombination only works with a few fragments, for now.... so... we would have to do sequencing. | 18:21 |
| kanzure | .title | 18:22 |
| yoleaux | International Journal of Proof-of-Concept or Get The Fuck Out (PoC||GTFO) | 18:22 |
| fenn | this is the 2600 spinoff i guess | 18:22 |
| kanzure | 0days just aren't what they used t obe | 18:23 |
| juul | ok. well that sounds like an interesting idea and also a massive undertaking :) | 18:23 |
| kanzure | juul: yeah i'm sure it would be a pain in the ass. but i'm pretty sure it will work. | 18:23 |
| juul | the latest issue has a very interesting article on LoRa reverse engineering | 18:23 |
| yashgaroth | your limit's like 1100 bp for fragment assembly of an antibiotic resistance gene + promoter, unless there's some enormous resistance gene out there | 18:23 |
| kanzure | yashgaroth: soo on the fragment length topic, i think we should assume it's 100 bp -- typical output of a DNA synthesizer. | 18:24 |
| kanzure | and also, antibiotic selection wouldn't wokr here.... let's say the cell has to assemble all 1,000 fragments correctly to get the antibiotic resistance genes. the chances of assembling all 1000 correctly is very low! | 18:24 |
| juul | yashgaroth: yes though there might be hacks, e.g. for bacteria putting a bunch of resistance markers on the same mRNA | 18:25 |
| yashgaroth | true, you can go up to 3 simultaneous resistance genes for sure, maybe a couple more if that's all the bacteria have to do | 18:26 |
| kanzure | if you want to split the resistance gene across many fragments, you can add some wacky promoters or put it behind some wacky regulatory network | 18:26 |
| yashgaroth | it's not great for 100+ fragments, but if you're just selecting for a cell that's better at assembly, then it's a start | 18:27 |
| fenn | so the idea is to let evolution do the work of figuring out how to assemble oligos into genes? | 18:28 |
| fenn | by making a good assembler-phenotype bacterium/yeast/whatever | 18:29 |
| kanzure | homologous recombination already does that... on a small scale. idea is to use evolution to select for cells that are even better at homologous recombination. | 18:29 |
| yashgaroth | yeah, but getting multiple generations of them is tricky since you run out of unique resistances pretty quick and they might just hold onto the genes | 18:29 |
| kanzure | yashgaroth: ah.... yes, well, that is why we need unique dna fragments for every round of selection. can't reuse the same fragments. | 18:29 |
| kanzure | (yes i know this sucks a lot) | 18:30 |
| juul | a rapid selection pipeline where the selection criteria includes the output of any kind of not 100% biology (e.g. a sequencer) is basically a magic "get me what i want" machine | 18:30 |
| kanzure | a grad student? | 18:30 |
| yashgaroth | and/or robot | 18:30 |
| juul | it's certainly what Amyris and Ginkgo BioWorks do | 18:31 |
| juul | btw have you seen the ginkgo bioworks t-shirts? :p | 18:31 |
| yashgaroth | grad students are still cheaper than robots if you promise them papers | 18:31 |
| juul | it's the Jurassic Park logo, except it says Ginkgo Bioworks instead of Jurassic Park, and then on the back: "There will be dragons..." | 18:32 |
| yashgaroth | "there will be yeast that smell sorta like roses" is a lot less motivating | 18:32 |
| kanzure | well that's why cambrian was going for vaginal rose infections or whatever | 18:33 |
| yashgaroth | anyway yeah having an entirely cell-based system is appealing since you could run it for a year and pull out magic bacteria, but we'll probably end up having to push millions of samples through some sort of machine instead | 18:35 |
| kanzure | probably at this point i should just give up and build a generic cell evolution system anyway..... | 18:35 |
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| yashgaroth | cells are such pains to work with, always concerned with their own survival...like c'mon I have needs too okay | 18:38 |
| kanzure | i think cellular selection is better than direct protein stuff, since cells have so many other components to work with-- more room for mutations and more room for other components to positively contribute to desired behaviors | 18:42 |
| yashgaroth | in theory it's far more elegant, since cells take care of their own propagation, but if you need to have constant feedback from an outside instrument anyway, like juul said, the advantages wear off | 18:45 |
| kanzure | yes... i was thinking of an emulsion droplet system, where each cell can be individually tracked. so there's no bulk bioreactor culture with cross-contamination from large populations or whatever. | 18:46 |
| yashgaroth | and more components means more things to go wrong, which is true everywhere but especially biology | 18:46 |
| yashgaroth | live-cell emulsion sounds tricky, but there's always FACS if you can modify the selection to work with that | 18:47 |
| kanzure | are most cell emulsions only dealing with dead cells? | 18:47 |
| yashgaroth | tbh I haven't looked into it much, I guess cells with walls might be okay in that environment | 18:48 |
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| yashgaroth | but most emulsion droplet stuff I' | 18:50 |
| yashgaroth | ve seen is just PCR | 18:50 |
| kanzure | oh. | 19:03 |
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| yashgaroth | not to say doing it reliably with live cells isn't doable, with the magic of ~microfludics~ or w/e, but it's not a mature field | 19:04 |
| kanzure | if the concern is food, you could put food in dissolvable caplets that take different amounts of time for a food schedule, inside each emulsion droplet | 19:05 |
| yashgaroth | they're not going to die quickly without food, especially single-celled organisms, but that's one of the concerns | 19:07 |
| kanzure | is it... cell membrane integrity? | 19:12 |
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| yashgaroth | there's that, which is way I say they'd need a cell wall, but otherwise...if they're only in droplets for a few hours maybe they'd be okay, but more than that and there just hasn't been much research on it | 19:17 |
| kanzure | hrm. | 19:19 |
| kanzure | i was not aware of this | 19:20 |
| kanzure | and what makes the microfluidic magic work? | 19:20 |
| yashgaroth | idk, I just assume microfluidics is magic and will solve everything, that's what people tell me | 19:21 |
| kanzure | and all this time i thought laminar flow was a hygiene product... | 19:21 |
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| yashgaroth | I'm sure we could get it to work, but it's only a technique until you have a robust system of selection/screening and evolution | 19:25 |
| yashgaroth | this is why I prefer grey-market biopharma, since you haven't necessarily had 400 screaming grad students overanalyze the field to death and still come up with bupkis; as is the case with most published fields | 19:27 |
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| kanzure | yeah this is sad news. i'll have to figure that out. | 19:52 |
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