--- Log opened Mon Jun 11 00:00:43 2018
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03:56 < adlai> kanzure: please document your bad idea so that other brains can decide on its badness for themselves
03:56 < adlai> the worst thing that'll happen is that they'll all decide you're Max Bad and you'll get loads of free publicity
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03:58 < adlai> fenn: that's a funny thing, and exactly why i sketch monochrome. complex matters such as palette selection are best left to assistants, apprentices, and artificialintelligences
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04:20 < aedla> dna synthesis price of $0.2/bp seems high.. why is it so high? is it the reagents that are expensive?
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04:24 < aedla> with posam, as I understand it, the estimated price was $25 / (9800 * 25) bp
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06:51 < kanzure> aedla: reagents expensive + large volumes + quality assurance costs and dna sequencing
06:51 < kanzure> and also need to run a business, margins, etc.
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06:56 < kanzure> "Practical constant-size ring signature" https://link.springer.com/article/10.1007/s11390-018-1838-z
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07:04 < kanzure> $0.20/bp is very high, i think industry is around $0.03/bp these days
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07:25 < aedla> kanzure: okay, but from the posam article, it should be $0.0001/bp, even with expensive phosphoramidite reagents
07:26 < aedla> are commercial services using large reaction volumes, not inkjet?
07:32 < kanzure> many suppliers are using old-school column-based synthesizers
07:32 < kanzure> some are doing array-based synthesis such as twist bioscience, agilent(?), genscript
07:32 < kanzure> twist has its own custom hardware for growing oligos on semiconductor wafers, about $25k of product per chip
07:33 < kanzure> here is a summary of a dna synthesis workshop that i wrote with nmz787 and another coauthor http://diyhpl.us/~bryan/dna-data-storage-workshop-summary-report.draft.2017-10-26.pdf
07:39 < aedla> thanks!
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08:17 < kanzure> aedla: so what's your interest in it
08:35 < aedla> kanzure: mostly procrastinating with tomorrow's exam
08:35 < aedla> wondering about possible cheaper and faster alternatives to synthesis
08:36 < aedla> and trying to understand the current bottlenecks for cost and speed and dna length and errors
08:44 < kanzure> aedla: well, i have one method for dna data storage (not biologically-relevant synthesis) that is significantly faster, using an enzymatic method
08:46 < kanzure> if you could control an enzyme and also get an enzyme to work on a loop of dna (maybe threaded through a nanopore or something) then you could run it in a circle until it fixes everything to be the sequence you wanted
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08:46 < kanzure> which would be able to support biologically-relevant synthesis. unfortunately in practical terms i've only figured out enzyme-based synthesis for dna data storage.
08:47 < kanzure> as soon as you start adding nanopores and nanowhatevers to your scenario, you're digging yourself deeper
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09:03 < aedla> kanzure: I'm confused. which enzyme do you mean? how do you control it?
09:04 < kanzure> :-)
09:04 < kanzure> those are good questions
09:05 < aedla> I wonder if you can make light switchable poly(A) pol with azobenzene
09:06 < kanzure> yeah maybe.. or electrical control: http://diyhpl.us/~bryan/irc/2017-02-03-beacon.pdf#page=24
09:06 < kanzure> my method doesn't use electrical or optical control, unfortunately
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09:18 < aedla> kanzure: that electrical control is nice
09:18 < aedla> anw, the 4^8 library approach seems nice and simple. the only drawback is maintaining the library?
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09:20 < kanzure> aedla: there's a related proposal to that library approach like http://engineeringbiologycenter.org/wp-content/uploads/2017/10/Berry-IA-Pilot-Project.pdf
09:42 < aedla> kanzure: this looks a lot simpler than TdT and capped nucleotides
09:46 < aedla> I was thinking of a similar thing with 5^4 library but an additional restriction after ligase
09:47 < aedla> er.. 4^5
09:51 < yashgaroth> ligase is unreliable with oligos shorter than 8bp, but it depends on how small we can get each spot on the array...4^8 means a lot of spots
09:51 < kanzure> aedla: this is a good TdT review i think, http://diyhpl.us/~bryan/papers2/DNA/Template-independent%20enzymatic%20oligonucleotide%20synthesis%20(TiEOS):%20Its%20history,%20prospects,%20and%20challenges%20-%202018.pdf
09:53 < yashgaroth> also re my pilot project proposal, the author's masters' thesis has a lot more info https://open.library.ubc.ca/media/stream/pdf/24/1.0068440/1
09:54 < yashgaroth> (author of the paper it's based on, that is)
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10:09 < aedla> Thanks!
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11:20 < archels> > Yeah I imagine it’s much easier for animals to recognize individuals of their own species than individuals of another. e.g. Humans have specialized brain circuitry for recognizing human faces, but all horse or bird faces basically look the same to us. A bird might easily think all humans look basically the same but obviously each bird is totally different.
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11:24 < kanzure> all your biological faces don't look like much of anything to me
11:25 < kanzure> https://i.pinimg.com/736x/c3/ef/aa/c3efaabe450c67809926bf571b835336--fashion-mask-sci-fi-fashion.jpg
11:43  * archels takes the retro-encabulator to kanzure's brain circuits
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13:39 < kanzure> yeah those retro-encafabulators really hurt
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13:53 < emeraldgreen> archels I doubt that there is selective species-specific circuitry, I think it is more of a bias (an experiment with three dots in an inverted triangle pattern shown to a child shows that child attends to this object like to a human face) and a mechanism to learn lots and lots of imprints starting from this bias. TLDR; Humans just have a super-crude face detector, see lots of humans while growing up and bottstrap their face classi
13:53 < emeraldgreen> fier from that. Interestingly the same area is active while looking at car faces
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14:43 < archels> .wik fusiform face area
14:43 < yoleaux> "The fusiform face area - FFA (meaning: spindular/spindle-shaped face area) is a part of the human visual system that is specialized for facial recognition. It is located in the Inferior temporal cortex (IT), in the fusiform gyrus (Brodmann area 37)." — https://en.wikipedia.org/wiki/Fusiform_face_area
14:43 < archels> you could argue it's much more nurture than nature
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17:03 < nmz787> https://hackaday.com/2018/05/22/smiling-robot-moves-without-wires/
17:03 < nmz787> https://hackaday.com/2014/04/23/micro-robots-are-scary-awesome/
17:03 < nmz787> https://hackaday.com/2015/08/18/ferrofluid-clock-is-a-work-of-art/
17:04 < nmz787> microbots for chemistry?
17:05 < nmz787> maybe they could have a little spear to jab liquids and move things around
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17:14 < kanzure> http://dinosaurpictures.org/ancient-earth#400
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17:47 < kanzure> https://mobile.nytimes.com/2018/06/10/us/11retro-baby-genetics.html
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18:29  * kanzure snaps his finger
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18:37 < nmz787> pretty sweet
18:38 < nmz787> guess I should call jeff steinberg for pgd for the next kid, and ask about intelligence selection and CRISPRing... idk, GFP?
18:40 < kanzure> plesae figure out the pricing from genomicprediction.com
18:40 < kanzure> and let me know
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19:30 < kanzure> http://www.juvenescence.ai/
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19:37 < kanzure> .wik adansonia grandidieri
19:37 < yoleaux> "Adansonia grandidieri, sometimes known as Grandidier's baobab, is the biggest and most famous of Madagascar's six species of baobabs. This imposing and unusual tree is endemic to the island of Madagascar, where it is an endangered species threatened by the encroachment of agricultural land." — https://en.wikipedia.org/wiki/Adansonia_grandidieri
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20:02 < kanzure> https://opentoonz.github.io/e/
20:05 < kanzure> https://krita.org/en/
20:15 < kanzure> lego thing https://studio.bricklink.com/v2/build/studio.page
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--- Log closed Tue Jun 12 00:00:44 2018