| --- Log opened Tue Jun 30 00:00:56 2015 | ||
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| delinquentme | kanzure, awake? | 01:00 |
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| eleitl | Morning. | 02:47 |
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| kanzure | does the brain make noise | 04:41 |
| kanzure | eleitl: would you be willing to rob some graves for me? it's important | 04:42 |
| eleitl | Which graves? | 04:50 |
| kanzure | smart dead people | 04:53 |
| * eleitl is listening | 05:02 | |
| kanzure | just want their genomes | 05:03 |
| eleitl | It's likely degraded. You should look for hair samples, and such. | 05:05 |
| archels | don't forget to keep the bacteria and other microorganisms for Aubrey | 05:06 |
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| kanzure | eleitl: skeletal dna can survive for quite a while | 05:38 |
| kanzure | archels: why? | 05:38 |
| archels | because he can repurpose their breakdown enzymes and machinery to rid living bodies of waste products | 05:45 |
| archels | (allegedly) | 05:45 |
| kanzure | was this something that he claimed/said? | 06:15 |
| kanzure | and why would it be "living bodies"? | 06:18 |
| archels | y'know, clear out some amyloid-β from otherwise healthy brains | 06:34 |
| archels | I think he said this in some documentary somewhere | 06:34 |
| 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 | 06:35 |
| 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 | 06:37 |
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| 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 | 06:40 |
| kanzure | it would also be nice to get an estimate of the amount of environmental dna for common soil samples | 06:41 |
| 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]." | 06:42 |
| kanzure | [3] is "Ancient DNA reveals late survival of mammoth and horse in interior Alaska" http://www.pnas.org/content/106/52/22352.short | 06:43 |
| 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. " | 06:44 |
| 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 | 06:56 |
| 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 | 06:58 |
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| heath | .title http://journal.frontiersin.org/article/10.3389/fnins.2015.00217/abstract | 07:04 |
| yoleaux | Frontiers | Brain-to-text: decoding spoken phrases from phone representations in the brain | Neural Technology | 07:05 |
| kanzure | meh, again | 07:05 |
| heath | didn't see your first meh, why the mehing? | 07:06 |
| kanzure | well at minimum the extremely high error rate | 07:07 |
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| eudoxia | kanzure: will bitcoin go to the moon because of this whole situation in greece | 08:31 |
| kanzure | nope, although if italy and spain follow then things might get interesting | 08:33 |
| kanzure | or puerto rico | 08:33 |
| eudoxia | hmm spain is a basket case | 08:41 |
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| 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 | 11:32 |
| 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 | 11:36 |
| CaptHindsight | no news about Kilobaser in about a year | 11:42 |
| 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 | 11:48 |
| 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 | 11:49 |
| 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 | 11:50 |
| CaptHindsight | yes both need some work | 11:51 |
| 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 | 11:52 |
| 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 | 11:53 |
| 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 | 11:55 |
| CaptHindsight | one thing to look at is making a library of short segments to assemble into longer ones | 11:56 |
| kanzure | yep... | 11:56 |
| CaptHindsight | but using a DMD or LCD is also slow since the reactions are at glacial speeds | 11:57 |
| CaptHindsight | beads are just segments of oligos | 11:58 |
| kanzure | theoretically, besides polymerase enzymes, another fast method of dna synthesis would be molecular nanotechnology | 11:59 |
| CaptHindsight | the replicator | 12:00 |
| CaptHindsight | just for DNA | 12:00 |
| 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 | 12:01 |
| CaptHindsight | would you call a carpenter to install your plumbing or electric? | 12:02 |
| CaptHindsight | that is the main problem I see | 12:02 |
| kanzure | i'd prefer an electrician; they know their shit. | 12:03 |
| CaptHindsight | but they probably wouldn't frame your house as well | 12:03 |
| CaptHindsight | there doesn't seem to be much cooperation between physicists and bio | 12:04 |
| kanzure | particle accelerator dna synthesis is unlikely to work | 12:04 |
| CaptHindsight | why is that? | 12:07 |
| CaptHindsight | Robert A. Freitas, Jr. was a Research Scientist at Zyvex Corp. | 12:09 |
| 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/ | 12:10 |
| 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 | 12:11 |
| CaptHindsight | I'm still trying to see what the problem is | 12:12 |
| 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 | 12:13 |
| eudoxia | kanzure: oh, the collaboration with that russian university? | 12:14 |
| 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 | 12:15 |
| 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? | 12:16 |
| 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? | 12:17 |
| 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 | 12:18 |
| 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 | 12:19 |
| 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 | 12:20 |
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| CaptHindsight | with what opportunities it will open up | 12:21 |
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| kanzure | sure | 12:21 |
| 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? | 12:22 |
| 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 :-) | 12:23 |
| kanzure | what was your complaint about micromirror array approaches? | 12:24 |
| 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 | 12:25 |
| 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. | 12:35 |
| CaptHindsight | the DMD stuff is just light directed/activated | 12:37 |
| CaptHindsight | also easy to construct | 12:37 |
| CaptHindsight | the chemistry part is still slow | 12:38 |
| CaptHindsight | the DMD version makes smaller samples | 12:39 |
| CaptHindsight | and it's easy to stitch DMD's to make more samples on the same sample tray | 12:40 |
| 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. | 12:41 |
| 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 | 12:42 |
| 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 | 12:43 |
| 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? | 12:44 |
| CaptHindsight | so all you're really doing is printing the resist as you go | 12:45 |
| CaptHindsight | be back later | 12:46 |
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| CaptHindsight | false alarm, back early | 13:07 |
| kanzure | howdy | 13:07 |
| CaptHindsight | maybe we should print everything | 13:07 |
| CaptHindsight | embed electronics into microfluids | 13:08 |
| CaptHindsight | sorry microfluidics | 13:08 |
| 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 | 13:09 |
| 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 | 13:10 |
| 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 | 13:11 |
| 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 | 13:12 |
| 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? | 13:13 |
| 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 :-) | 13:14 |
| CaptHindsight | if the valves were in the fluid channels they may be reused and be digitally controlled | 13:15 |
| kanzure | that's not the problem with microvalves -_- | 13:16 |
| CaptHindsight | I'm just thinking about what is gained by this approach | 13:16 |
| 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 | 13:17 |
| kanzure | cool | 13:18 |
| kanzure | valveless microfluidics is easier and also possible | 13:18 |
| kanzure | (continuous flow stuff) | 13:18 |
| kanzure | hmm the transcriptic.com video that i uploaded to youtube has been blocked by aol | 13:24 |
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| 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 | 15:35 |
| kanzure | criticism http://femsle.oxfordjournals.org/content/353/2/85.full | 15:36 |
| 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)." | 15:37 |
| kanzure | "The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils" http://rspb.royalsocietypublishing.org/content/279/1748/4724.short | 15:40 |
| ryankarason | :o | 15:43 |
| kanzure | .title http://www.pnas.org/content/110/49/19860.short | 15:45 |
| 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! | 15:46 |
| kanzure | response to the criticism http://femsle.oxfordjournals.org/content/femsle/353/2/87.full.pdf | 15:49 |
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| kanzure | hmph | 16:36 |
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| archels | kanzure: I find the original criticism quite damning, and the response really weak | 16:52 |
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| CaptHindsight | http://cen.acs.org/articles/93/web/2015/06/Microfluidic-Device-Mixes-Matches-DNA.html | 17:45 |
| kanzure | CaptHindsight: http://diyhpl.us/~bryan/papers2/microfluidics/synthesis/ | 17:46 |
| kanzure | CaptHindsight: http://diyhpl.us/~bryan/papers2/microfluidics/ | 17:46 |
| CaptHindsight | anything new there? | 17:47 |
| kanzure | you read them all already? | 17:47 |
| kanzure | not surprised i guess | 17:47 |
| CaptHindsight | what I often find is that researchers aren't racing to invent but just pacing themselves to keeping the funding coming in | 17:52 |
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| CaptHindsight | and it looks like they also use some type of accounting mainly used in the motion picture industry | 17:52 |
| CaptHindsight | http://www.sandia.gov/biosystems/anup/ | 17:55 |
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| --- Log closed Wed Jul 01 00:00:57 2015 | ||
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