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05:35 < kanzure> darwin is making a cryonics facility
05:36 < chris_99> Mike Darwin?
05:38 < kanzure> yes....? do we know other darwins?
05:38 < chris_99> is there any evidence that cryopreservation of humans may actually work?
05:45 < kanzure> depends on what you mean by "works"
05:50 < kanzure> so far we have not demonstrated cryoresuscitation of humans
05:50 < kanzure> however, we have demonstrated cryoresuscitation of worms
05:53 < 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
05:57 < kanzure> .. and various selection projects...
05:59 < kanzure> and as for thresholds for defining 'working', i think that 5% memory survival and only partial personality would still be tremendously useful.
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06:20 < chris_99> 5% seems very low doesn't it?
06:29 < kanzure> compared to 0, i'd take it
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06:49 < kanzure> __mz_o: the abi 391 pcr-mate manual is available here, http://diyhpl.us/~bryan/papers2/DNA/abi391/
06:53 < __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?
06:55 < kanzure> the one i bought was <$500, if you're making lots of primers i guess that's okay
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07:15 < __mz_o> the price is what had caught my attention
07:16 < __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
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07:19 < __mz_o> i know you can run custom cycles, could this synthesize peptides given the proper cycle/reagents?
07:20 < 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/
07:24 -!- darsie is now known as bad
07:25 < 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.
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07:27 < 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
07:28 < 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.
07:30 < juri_> this has been quite a challenge. thanks for starting me down this path. :)
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07:35 < __mz_o> kanzure: thanks for pointing me to the synthesis notes. Makes understanding the manual a little better
07:36 < __mz_o> I guess i have to scour and sift through the wiki sometime soon
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07:36 < __mz_o> juri_: one would think that youre rendering the universe! lol
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07:47 < CaptHindsight> kanzure: synthesizing genes for MRO (Maintenance, Repair and Operations) of organisms was my interest
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07:48 < __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
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07:49 < __mz_o> gotta find the full version somewhere
07:50 < kanzure> CaptHindsight: gibson assembly can already put together entire genes, that's doable with modern techniques.
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07:52 < CaptHindsight> kanzure: I was looking at something like 24 hour turn custom mods
07:53 < kanzure> well, you would need virus manufacturing. the slow parts are DNA sequencing and validation of the synthesized fragments.
07:54 < 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
07:55 < CaptHindsight> but after the last election I'm not sure about making it easily available
07:56 < 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
07:57 < 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
07:58 < kanzure> i have not looked into the actual equipment pipeline required for virus manufacturing
07:59 < CaptHindsight> the tech seems to be scattered across several players and patents
08:00 < 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)
08:01 < __mz_o> he has/manages the lab or is just sending work to the lab?
08:02 < 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
08:12 < CaptHindsight> CRISPR trials on humans has already started in China
08:13 < CaptHindsight> University of Pennsylvania starts their trials next year
08:14 < CaptHindsight> I wonder what they have planned for DNA synthesis at the Parker Institute for Cancer Immunotherapy?
08:15 < kanzure> probably just outsourcing it
08:15 < kanzure> nobody cares about synthesis :(
08:15 < CaptHindsight> The National Cancer Institute (NCI) still outsources theirs
08:16 < CaptHindsight> they are looking at finally doing it in house
08:22 < 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
08:29 < 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?
08:30 < kanzure> hm?
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08:31 < CaptHindsight> or let things play out since the earth is overpopulated
08:32 < 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
08:36 < kanzure> __mz_o: he owns the lab. or rather, he set it up. something like that. not outsourcing.
08:37 < CaptHindsight> is there a secret underground bunker at the CDC that already has the defense tech?
08:41 < kanzure> there's prolly some military stuff somewhere
08:42 < 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.
08:46 < CaptHindsight> sounds like an opportunity
08:46 < CaptHindsight> just needs some fake news to to generate interest
08:47 < kanzure> "please panic because: government is hiding anti-virus tech from you"?
08:49 < CaptHindsight> bad guys can make bad stuff, we need a quick defense system
08:51 < CaptHindsight> duct tape won't save you this time
08:52 < CaptHindsight> didn't save you last time either since only a few scary packages were publicized
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09:21 < CaptHindsight> https://www.genomeweb.com/sequencing-technology/oxford-nanopore-releases-pricing-minion-flow-cells-users-publish-new-data
09:22 < 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
09:23 < 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
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09:42 < aedla> I wonder why the flow cells have a maximum yield.. Nanopores get damaged over time?
09:44 < kanzure> maybe there are problems with sample prep
09:44 < CaptHindsight> maybe they made theirs in a way that wears
09:45 < CaptHindsight> look at the business model
09:45 < CaptHindsight> this keeps the cash flowing with a consumable
09:46 < CaptHindsight> now there is a patent battle between Oxford and illimina
09:47 < CaptHindsight> http://www.bio-itworld.com/2016/2/24/illumina-sues-oxford-nanopore-technologies-over-composition-nanopores.html
09:48 < CaptHindsight> why it wears  https://nanoporetech.com/how-it-works
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10:25 < aedla> the how-it-works page is interesting. I still don't get why it wears. although yeah, maybe just a business model
10:26 < CaptHindsight> they appear to use a polymer membrane nanopore
10:27 < CaptHindsight> ?-hemolysin is a heptameric protein pore with an inner diameter of 1 nm
10:28 < CaptHindsight> not tough like SiO2
10:29 < CaptHindsight> or graphene
10:34 < aedla> right.. and there's probably tons of stuff that can damage the protein pore over time, like radiation and oxygen?
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11:25 < nmz787_w> sup
11:26 < nmz787_w> I've not read logs in 1.5 weeks or so
11:32 < 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
11:33 < nmz787_w> huh, the google image results for abi pcr mate are mostly from that take-apart
11:34 < 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
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11:35 < 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
11:37 < kanzure> plus they have expirations
11:38 < kanzure> so usage means you have to prep everything to be shipped at the same time (roughly)
11:41 < 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
11:42 < 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
11:43 < 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
11:44 < 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
11:45 < 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
11:46 < 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
11:47 < 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
11:48 < chris_99> cheers, i'll watch that with sound later
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13:04 < ybit> Farm Hack: worldwide community of farmers that build and modify our own tools https://news.ycombinator.com/item?id=13063541
14:05 < kanzure> http://gundam-challenge.com/
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15:27 < 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
15:28 < nmz787_w> "A 420lb propane tank is to serve as the sterilization chamber. "
15:30 < nmz787_w> welp, the wording of this event feels pretty disclusionary http://nesawg.org/events/women-sustainable-agriculture-conference
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15:42 < cluckj> no kidding? it's supposed to be
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16:03 < 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
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16:23 < cluckj> you should go
16:24 < cluckj> but like...just watch and listen
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17:02 < kanzure> don't bring that in here
17:02 < kanzure> got enough problems up in this joint
17:14 < 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
17:15 < 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
17:23 < kanzure> surely gundam has been around long enough that the robotics professors are all in the job because of the show
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18:06 < kanzure> yashgaroth: greetings
18:07 < kanzure> i am presently harassing juul about https://groups.google.com/d/msg/enzymaticsynthesis/uyZqtJO24RE/lApLb4JmCAAJ
18:07 < yashgaroth> hoi
18:10 < yashgaroth> oh yeah I should make a post there about the recombinase stuff
18:13 < kanzure> eh just link to the logs, close enough
18:14 < 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?
18:15 < 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?
18:17 < fenn> thanks for the summary
18:21 < 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.
18:22 < 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
18:23 < 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
18:24 < 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!
18:25 < juul> yashgaroth: yes though there might be hacks, e.g. for bacteria putting a bunch of resistance markers on the same mRNA
18:26 < 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
18:27 < 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
18:28 < fenn> so the idea is to let evolution do the work of figuring out how to assemble oligos into genes?
18:29 < 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.
18:30 < 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
18:31 < 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
18:32 < 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
18:33 < kanzure> well that's why cambrian was going for vaginal rose infections or whatever
18:35 < 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.....
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18:38 < yashgaroth> cells are such pains to work with, always concerned with their own survival...like c'mon I have needs too okay
18:42 < 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
18:45 < 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
18:46 < 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
18:47 < 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?
18:48 < yashgaroth> tbh I haven't looked into it much, I guess cells with walls might be okay in that environment
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18:50 < yashgaroth> but most emulsion droplet stuff I'
18:50 < yashgaroth> ve seen is just PCR
19:03 < kanzure> oh.
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19:04 < 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
19:05 < 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
19:07 < yashgaroth> they're not going to die quickly without food, especially single-celled organisms, but that's one of the concerns
19:12 < kanzure> is it... cell membrane integrity?
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19:17 < 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
19:19 < kanzure> hrm.
19:20 < kanzure> i was not aware of this
19:20 < kanzure> and what makes the microfluidic magic work?
19:21 < 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...
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19:25 < 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
19:27 < 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
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19:52 < kanzure> yeah this is sad news. i'll have to figure that out.
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--- Log closed Wed Nov 30 00:00:25 2016