--- Log opened Tue Jun 30 00:00:56 2015
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01:00 < delinquentme> kanzure, awake?
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02:47 < eleitl> Morning.
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04:41 < kanzure> does the brain make noise
04:42 < kanzure> eleitl: would you be willing to rob some graves for me? it's important
04:50 < eleitl> Which graves?
04:53 < kanzure> smart dead people
05:02  * eleitl is listening
05:03 < kanzure> just want their genomes
05:05 < eleitl> It's likely degraded. You should look for hair samples, and such.
05:06 < archels> don't forget to keep the bacteria and other microorganisms for Aubrey
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05:38 < kanzure> eleitl: skeletal dna can survive for quite a while
05:38 < kanzure> archels: why?
05:45 < archels> because he can repurpose their breakdown enzymes and machinery to rid living bodies of waste products
05:45 < archels> (allegedly)
06:15 < kanzure> was this something that he claimed/said?
06:18 < kanzure> and why would it be "living bodies"?
06:34 < archels> y'know, clear out some amyloid-β from otherwise healthy brains
06:34 < archels> I think he said this in some documentary somewhere
06:35 < kanzure> oh, but i was talking about the dead..?
06:35 < kanzure> and why would that those critters survive in the grave?
06:35 < archels> because they're breaking down dead bodies, so they're probably pretty good at that
06:37 < kanzure> sodium acetate precipitation seems to work for 9 month old bone material:
06:37 < kanzure> http://diyhpl.us/~bryan/papers2/DNA/A%20simple%20method%20for%20extracting%20DNA%20from%20old%20skeletal%20material.pdf
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06:40 < kanzure> we should make a method for simulating the effects of long-term dna storage in the ground, then focus on making enzymes that can be secreted into the soil to help preserve environmental dna it comes into contact with
06:41 < kanzure> it would also be nice to get an estimate of the amount of environmental dna for common soil samples
06:42 < kanzure> huh... "The term “environmental DNA” originated in the field of microbiology [1] – the science that studies microbes such as bacteria or algae. Microbiologists first detected and quantified eDNA in seawater, attempting to learn if the amount of DNA could be an indicator for the amount of plankton [2]. Since then, scientists have found eDNA in many different environments and from many different organisms, including permafrost soil ...
06:42 < kanzure> ... eDNA from mammoths that died 10,000 years ago [3]."
06:43 < kanzure> [3] is "Ancient DNA reveals late survival of mammoth and horse in interior Alaska" http://www.pnas.org/content/106/52/22352.short
06:44 < kanzure> "Here we report an alternative approach to detect ‘ghost ranges’ of dwindling populations, based on recovery of ancient DNA from perennially frozen and securely dated sediments (sedaDNA). In such contexts, sedaDNA can reveal the molecular presence of species that appear absent in the macrofossil record. We show that woolly mammoth and horse persisted in interior Alaska until at least 10,500 yr BP, several thousands of years later ...
06:44 < kanzure> ... than indicated from macrofossil surveys. "
06:56 < kanzure> weird, it seems that someone pcr'd the genome of the "angel of death" http://www.fsijournal.org/article/0379-0738(92)90148-P/abstract
06:58 < heath> .title http://neurosciencenews.com/brain-text-sentence-reconstruction-2126/
06:58 < yoleaux> Reconstructing Spoken Sentences From Brain Activity Patterns | Neuroscience News
06:58 < kanzure> meh
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07:04 < heath> .title http://journal.frontiersin.org/article/10.3389/fnins.2015.00217/abstract
07:05 < yoleaux> Frontiers | Brain-to-text: decoding spoken phrases from phone representations in the brain | Neural Technology
07:05 < kanzure> meh, again
07:06 < heath> didn't see your first meh, why the mehing?
07:07 < kanzure> well at minimum the extremely high error rate
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08:31 < eudoxia> kanzure: will bitcoin go to the moon because of this whole situation in greece
08:33 < kanzure> nope, although if italy and spain follow then things might get interesting
08:33 < kanzure> or puerto rico
08:41 < eudoxia> hmm spain is a basket case
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11:32 < CaptHindsight> after looking over all the DNA synthesizers it looks like hardly anyone is working on anything close to "rapid" or they are keeping it secret
11:36 < heath> ;first time i've heard of https://en.wikipedia.org/wiki/CERN_Open_Hardware_License
11:36 < heath> pointing someone to http://www.opencircuits.com/Open_hardware and http://www.oshwa.org/definition/ with fingers crossed they open up their bluetooth smart SoC
11:42 < CaptHindsight> no news about Kilobaser in about a year
11:48 < kanzure> CaptHindsight: cambrian genomics was doing something interesting, involving laser catapulting of microbeads and then sequencing
11:48 < CaptHindsight> kanzure: it was faster (an improvement) but still what I'd consider slow
11:49 < kanzure> much of the slow is because of reaction chemistry duration
11:49 < kanzure> parallelizing it will make it less slow overall
11:49 < kanzure> e.g. 100 million molecules in parallel
11:49 < kanzure> er i mean 100 million different combinations in parallel
11:49 < CaptHindsight> or speeding up the process
11:50 < CaptHindsight> yes, parallel is one way but it's clumsy
11:50 < kanzure> parallel is necessary
11:50 < CaptHindsight> you still have to stitch fragments together
11:50 < CaptHindsight> if you don't have other tech
11:50 < kanzure> machine design is not going to fix phosphoramidite chemistry
11:50 < kanzure> if you want to fix the chemistry that's fine but nobody has good ideas in that direction yet
11:51 < CaptHindsight> yes both need some work
11:52 < CaptHindsight> thats why it looks like nobody is working on this or it's being done in private
11:52 < CaptHindsight> Kilobaser seems to have gone silent after getting venture funding
11:52 < CaptHindsight> but that approach is also real slow
11:53 < kanzure> fastest method is using polymerase, except nobody knows how to electronically or optically control polymerase's selection of nucleotides
11:53 < CaptHindsight> I just thought that more people were working on this and if was far far further along than it appears to be
11:53 < CaptHindsight> if/it
11:55 < CaptHindsight> yes, you can make a giant inkjet printer farm to brute force making fragments in parallel
11:55 < kanzure> nah the highly parallel method is either a liquid crystal matrix display or a micromirror array
11:56 < CaptHindsight> one thing to look at is making a library of short segments to assemble into longer ones
11:56 < kanzure> yep...
11:57 < CaptHindsight> but using a DMD or LCD is also slow since the reactions are at glacial speeds
11:58 < CaptHindsight> beads are just segments of oligos
11:59 < kanzure> theoretically, besides polymerase enzymes, another fast method of dna synthesis would be molecular nanotechnology
12:00 < CaptHindsight> the replicator
12:00 < CaptHindsight> just for DNA
12:01 < CaptHindsight> whats the supposed hold up with that approach?
12:01 < kanzure> nobody knows how to construct the tooltips yet
12:01 < kanzure> http://diyhpl.us/~bryan/papers2/nanotech/
12:01 < kanzure> http://diyhpl.us/~bryan/papers2/nanotech/Optimal%20Tooltip%20Trajectories%20in%20a%20Hydrogen%20Abstraction%20Tool%20Recharge%20Reaction%20Sequence%20for%20Positionally%20Controlled%20Diamond%20Mechanosynthesis.pdf
12:02 < CaptHindsight> would you call a carpenter to install your plumbing or electric?
12:02 < CaptHindsight> that is the main problem I see
12:03 < kanzure> i'd prefer an electrician; they know their shit.
12:03 < CaptHindsight> but they probably wouldn't frame your house as well
12:04 < CaptHindsight> there doesn't seem to be much cooperation between physicists and bio
12:04 < kanzure> particle accelerator dna synthesis is unlikely to work
12:07 < CaptHindsight> why is that?
12:09 < CaptHindsight> Robert A. Freitas, Jr.   was a Research Scientist at Zyvex Corp.
12:10 < CaptHindsight> http://www.rfreitas.com./
12:10 < kanzure> freitas has written many interesting documents
12:10 < CaptHindsight> http://www.molecularassembler.com/  small world
12:10 < kanzure> "kinematic self-replicating machines" (KSRM) is also quite good http://www.molecularassembler.com/KSRM.htm
12:10 < kanzure> "advanced automation for space missions" (AASM) http://www.islandone.org/MMSG/aasm/
12:11 < kanzure> "xenology" (speculation about alien civilizations) http://www.xenology.info/
12:11 < CaptHindsight> I wonder how he got in involved in that Kazakhstan project
12:11 < kanzure> other way around
12:11 < kanzure> they got involved with him, iirc
12:12 < CaptHindsight> I'm still trying to see what the problem is
12:13 < kanzure> dna synthesis
12:13 < CaptHindsight> looks like funding and people working o it
12:13 < eudoxia> what did freitas do in kazakhstan?
12:13 < CaptHindsight> joint project in that pdf link ^^^^
12:13 < kanzure> eudoxia: freitas has some lakeys in russia
12:14 < eudoxia> kanzure: oh, the collaboration with that russian university?
12:15 < kanzure> CaptHindsight: btw this is both the eugen leitl *and* robert freitas fan club
12:15 < CaptHindsight> the other problem seems to be what to do with a synthesizer
12:15 < kanzure> there are many things to do with a dna synthesizer
12:15 < CaptHindsight> who gets their hands on it and for what purpose
12:15 < kanzure> well, an open-source design would mean that you don't have to decide that
12:15 < kanzure> or rather, that you are explicitly permissive
12:16 < kanzure> but for more practical purposes:
12:16 < kanzure> http://diyhpl.us/wiki/genetic-modifications/
12:16 < kanzure> http://diyhpl.us/wiki/dna/projects/#igem-2014
12:16 < CaptHindsight> yeah, like handing explosives out at a school yard, what could go wrong?
12:17 < kanzure> you must be terrified of people having sex on their own
12:17 < CaptHindsight> I wonder if that is the main reason for the lack of info
12:17 < kanzure> or terrified of cancer
12:17 < kanzure> "oh noes there's going to be a mutation that causes a plague~~~~" except it happens all the time; populations get sick. genome synthesis can help people heal faster.
12:17 < CaptHindsight> I must be? When did this get personal?
12:18 < kanzure> the moment you brought up your anxiety regarding bombs in schoolyards
12:18 < CaptHindsight> my anxiety?
12:18 < kanzure> you clearly indicated you wanted a discussion about this
12:18 < CaptHindsight> there's just so little published work on rapid DNA synthesis
12:18 < CaptHindsight> I'm wondering why
12:18 < kanzure> polymerase is extremely rapid
12:19 < CaptHindsight> lack of work or just private
12:19 < kanzure> lack of ideas
12:19 < CaptHindsight> or lack of public ideas?
12:19 < kanzure> that's impossible to determine, private ideas are unmeasurable
12:20 < CaptHindsight> yeah, what's your take, it's just not worked on much?
12:20 < kanzure> no idea
12:20 < CaptHindsight> just seems odd
12:20 < kanzure> anyway did you look at http://diyhpl.us/wiki/dna/projects/#igem-2014 has lots of stuff to do with genome synthesis
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12:21 < CaptHindsight> with what opportunities it will open up
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12:21 < kanzure> sure
12:22 < CaptHindsight> so open inkjet or laser printer?
12:22 < kanzure> er which one is the laser printer?
12:22 < CaptHindsight> or is there a patent on the laser approach?
12:23 < CaptHindsight> what Cambrian was/is doing
12:23 < kanzure> oh you mean cambrian genomic's catapulter? meh- it's helpful, for sure.
12:23 < CaptHindsight> laser launcher
12:23 < kanzure> much better name :-)
12:24 < kanzure> what was your complaint about micromirror array approaches?
12:25 < kanzure> too slow? isn't it the same speed as inkjet chemistry
12:25 < kanzure> actually- it doesn't matter- i think either one would be useful compared to neither at all
12:35 < kanzure> a chemical approach that i have considered in the past is to synthesize something like LNA or GNA instead of DNA/RNA/oligos... and then use the modified polymerases to convert back to something biologically-relevant. but so far i haven't been able to find a LNA/GNA alternative that seems particularly easy to chemically synthesize.
12:37 < CaptHindsight> the DMD stuff is just light directed/activated
12:37 < CaptHindsight> also easy to construct
12:38 < CaptHindsight> the chemistry part is still slow
12:39 < CaptHindsight> the DMD version makes smaller samples
12:40 < CaptHindsight> and it's easy to stitch DMD's to make more samples on the same sample tray
12:41 < kanzure> depending on optics you could just make a giant room-sized mirror array instead of micromirror array. then just shine light on each mirror, direct the light towards some surface somewhere in the room. could have as many elements as you need.
12:42 < kanzure> i think one of the reasons we haven't had much progress on the dmd front is because we don't have strong optics skillz in here
12:42 < CaptHindsight> I've been to Maker spaces and I don't trust them with welding equipment  :)
12:42 < kanzure> totally fair
12:43 < CaptHindsight> I'm looking at the wavelengths required for light based
12:43 < kanzure> http://diyhpl.us/~bryan/papers2/microfluidics/synthesis/Synthesis%20-%20Microfluidic%20PicoArray%20synthesis%20of%20oligodeoxynucleotides%20and%20simultaneous%20assembling%20of%20multiple%20DNA%20sequences%20(10%20kb).pdf
12:44 < kanzure> 405 nm
12:44 < kanzure> no wait
12:44 < kanzure> 532 nm and 635 nm
12:44 < CaptHindsight> any that the PI in the photoresist work with
12:44 < kanzure> hm no
12:44 < kanzure> hm?
12:45 < CaptHindsight> so all you're really doing is printing the resist as you go
12:46 < CaptHindsight> be back later
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13:07 < CaptHindsight> false alarm, back early
13:07 < kanzure> howdy
13:07 < CaptHindsight> maybe we should print everything
13:08 < CaptHindsight> embed electronics into microfluids
13:08 < CaptHindsight> sorry microfluidics
13:09 < CaptHindsight> micro-valves printed right into the fluid channels
13:09 < kanzure> valves are difficult to make and it increases the complexity of the designs
13:09 < CaptHindsight> nah easy peasy
13:10 < kanzure> yes it's easy in theory, but in practice.. as you increase the number of components of your system, the more debugging you have to do to get any of it to work.
13:10 < kanzure> this is why the pico paper (linked above) used an external valve system (not microfluidic)
13:10 < CaptHindsight> yeah been doin this for a while
13:10 < kanzure> that's not a good argument
13:11 < CaptHindsight> it's ok, it's not an argument
13:11 < kanzure> how many microvalves have you constructed and at what error rate?
13:11 < kanzure> and i'm also curious why you would claim they are far easier to make than what my estimates have been
13:12 < kanzure> conclusions should be drawn from evidence- i just want to hear your evidence or see what's up
13:12 < CaptHindsight> when you make the materials as well as the deposition tech things change
13:13 < kanzure> too vague
13:13 < CaptHindsight> well I can make whatever who is paying the bills wants
13:13 < kanzure> pneumatic valves (pressed pdms) and screw valves have both looked highly unreliable and hard to debug in microfluidics
13:13 < CaptHindsight> or I can do whatever I want
13:13 < CaptHindsight> which discussion are we having?
13:14 < kanzure> the one where you're trying to convince me that you know how to make microvalves work better than everyone else
13:14 < kanzure> it's possible that you know how to do it, so that's why i'm listening :-)
13:15 < CaptHindsight> if the valves were in the fluid channels they may be reused and be digitally controlled
13:16 < kanzure> that's not the problem with microvalves -_-
13:16 < CaptHindsight> I'm just thinking about what is gained by this approach
13:17 < kanzure> apparently i am bad at conveying to you that "we have spent a lot of time evaluating design options with microvalves and the prospects are not great"
13:17 < CaptHindsight> no you made your point clear
13:18 < kanzure> cool
13:18 < kanzure> valveless microfluidics is easier and also possible
13:18 < kanzure> (continuous flow stuff)
13:24 < kanzure> hmm the transcriptic.com video that i uploaded to youtube has been blocked by aol
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15:35 < kanzure> "Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber" http://www.sciencemag.org/content/268/5213/1060.short
15:36 < kanzure> criticism http://femsle.oxfordjournals.org/content/353/2/85.full
15:37 < kanzure> "... however, they fail to mention the wealth of publications demonstrating the opposite – that DNA alone could not be obtained from copal (unfossilized amber) only 10 000 years old (Austin et al., 1998) or that identifiable DNA fragments, let alone nonreplicating microorganisms, do not persist beyond 1.5 million years (Allentoft et al., 2012)."
15:40 < kanzure> "The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils" http://rspb.royalsocietypublishing.org/content/279/1748/4724.short
15:43 < ryankarason> :o
15:45 < kanzure> .title http://www.pnas.org/content/110/49/19860.short
15:46 < yoleaux> Bacterial natural transformation by highly fragmented and damaged DNA
15:46 < delinquentme> who do we have whos adept as shit at yeast transformations?
15:46 < delinquentme> jinx!
15:49 < kanzure> response to the criticism http://femsle.oxfordjournals.org/content/femsle/353/2/87.full.pdf
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16:36 < kanzure> hmph
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16:52 < archels> kanzure: I find the original criticism quite damning, and the response really weak
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17:45 < CaptHindsight> http://cen.acs.org/articles/93/web/2015/06/Microfluidic-Device-Mixes-Matches-DNA.html
17:46 < kanzure> CaptHindsight: http://diyhpl.us/~bryan/papers2/microfluidics/synthesis/
17:46 < kanzure> CaptHindsight: http://diyhpl.us/~bryan/papers2/microfluidics/
17:47 < CaptHindsight> anything new there?
17:47 < kanzure> you read them all already?
17:47 < kanzure> not surprised i guess
17:52 < CaptHindsight> what I often find is that researchers aren't racing to invent but just pacing themselves to keeping the funding coming in
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17:52 < CaptHindsight> and it looks like they also use some type of accounting mainly used in the motion picture industry
17:55 < CaptHindsight> http://www.sandia.gov/biosystems/anup/
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--- Log closed Wed Jul 01 00:00:57 2015