--- Log opened Fri Nov 17 00:00:17 2017
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05:23 < kanzure> fenn: maybe techshop should have had higher prices?
05:45 < kanzure> .title https://www.youtube.com/watch?v=5n9xafjynJA
05:45 < yoleaux> Tesla Semi truck and Roadster event in 9 minutes - YouTube
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06:26 < kanzure> the magic of tesla preorders https://news.ycombinator.com/item?id=15719882
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07:10 < pasky_> I understand when people preorder their cars. But will any company preorder a fleet of trucks?!
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08:31 < heath> .title https://www.youtube.com/watch?v=5n9xafjynJA
08:31 < yoleaux> Tesla Semi truck and Roadster event in 9 minutes - YouTube
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10:01 < kanzure> .title https://endpoints.elysiumhealth.com/george-church-profile-4f3a8920cf7g-4f3a8920cf7f
10:01 < yoleaux> George Church Will Make Virus-Proof Organisms, Transplant Pig Organs to Humans, and Reverse Aging
10:03 < kanzure> "We’ve brought down the cost and price of many things including reading the genome by three million fold. Writing synthetic oligonucleotides, even bigger than that. Editing is more modest: maybe 100 fold. But I think we can do it. I don’t see any particular reason why a biological can’t be made inexpensively. It boils down to how much the clinical trials cost and over what size ...
10:03 < kanzure> ...population can you amortize the cost of the trials. If you have a small trial that works on a huge population, you’re going to get your money back quickly. So things like aging, it’s a potential population of 7.5 billion people, in contrast to something that cures, say, a particular eye disease like LCA that we’re doing at Editas, that could be one in a million. One way to bring down ...
10:03 < kanzure> ...the price is keep the studies small by having something that has a high intrinsic safety and having the population it affects be large. I’m very dedicated to it. But certainly the history of pharmaceuticals is the opposite. Costs keep creeping up. I think that could change."
10:05 < kanzure> .tw https://twitter.com/petertoddbtc/status/931563003501309952
10:05 < yoleaux> @kanzure @jgarzik For the record, I think it's really toxic how @pwuille, Gregory Maxwell, Andrew Poelstra, etc. keep making me look bad with all their brilliant hard work on math-intensive things like libsecp256k1 and Confidential Transactions. (@petertoddbtc, in reply to tw:931550576487337985)
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10:40 < maaku> kanzure: while planning what to say in that meeting you setup for me in 20min, I realized that Merkle and Freitas should be doing a nanofactory patent pool ICO
10:40 < maaku> that's financial engineering that would work
10:41 < maaku> raise a big pool of money by selling shares in the patent pool to be created from the research done with that money
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10:42 < maaku> pasky_: it depends on if it really does cut costs. but with tesla's reliability (or lack thereof), I doubt they will get many corporate bids
10:42 < maaku> s/bids/pre-orders/
10:42 < maaku> but on the other hand, many truckers own their own semis
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10:45 < MrHindsight> sounds like kickstarter  :)
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10:48 < kanzure> maaku: not sure they want to sell their patents
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11:08 <@fenn> techshop should have given people X minutes of free laser cutter time and then charged them a reasonable usage fee after that
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11:21 < MrHindsight> there are tech incubators in the Chicago area that charge similar to Tech Shop
11:21 < MrHindsight> looks like they just had poor management
11:23 < MrHindsight> how do you balance having machines that can kill you with hobbyists?
11:23 <@fenn> yeah they hired a bunch of greedly clueless business people to rape and pillage the generosity of people who would otherwise have started their own hackerspace
11:24 < MrHindsight> wonder what the insurance rates were
11:25 < MrHindsight> fenn: I'm seeing fragmentation in the makerspaces in this area
11:25 <@fenn> is that bad?
11:25 < MrHindsight> there used to be one, now there are several that split and took their equipment with them
11:25 <@fenn> it seems to me that getting the equipment is relatively easy
11:26 <@fenn> keeping shit running is the hard part
11:26 < MrHindsight> to much jr high behavior
11:26 < MrHindsight> they even had a SEM
11:26 < MrHindsight> I used to drop by...
11:27 < MrHindsight> lots of drama
11:28 < gradstudentbot> If you help me, I'll put you on the paper.
11:28 < MrHindsight> yeah basic tools, power tools yeah, just run down to Home Depot
11:28 <@fenn> companies will donate stuff, you can get it for nothing at auctions etc
11:29 < MrHindsight> the CNC's, SLA printer, vacuum former etc lay idle
11:29 < MrHindsight> yeah they had tons of donations, scopes, logic analyzers, meters etc
11:30 <@fenn> the scarcest resource at most "makerspaces" is people who want badly enough to do things that they will teach themselves how to do it
11:30 <@fenn> i see a lot of people who just show up for socialization, which is okay and all, but it's not why you put a bunch of equipment in a shared room
11:31 < MrHindsight> as long as it doesn't get toxic
11:31 <@fenn> hmm what do you think about a hackerspace with like, absolutely no couches or chairs anywhere
11:32 < MrHindsight> BYOC?
11:32 <@fenn> no, i mean, you're there to do stuff, not sit around and be a presence
11:33 < MrHindsight> heh, well at this one you couldn't walk away from your open laptop without some prank being pulled on you
11:33 < MrHindsight> I didn't see this behavior in other cities or countries...
11:33 < MrHindsight> so maybe it's a Chicago thing
11:34 <@fenn> drama is unfortunately very common
11:34 < MrHindsight> the sitting and chatting parts is great if there is an actual exchange of ideas and info
11:35 < MrHindsight> not if it's like a jr high lunchroom
11:36 <@fenn> i can't even remember my jr high lunchroom
11:38 < MrHindsight> the Tech Spaces in other countries are still in business
11:38 < MrHindsight> separate management
11:39 <@fenn> i'm hoping people will pull together to purchase the buildings and equipment for at least some of them
11:39 < MrHindsight> brewing beer was a big hit
11:40 <@fenn> beer?
11:40 <@fenn> at your hackerspace?
11:40 < MrHindsight> a pick-n-place project went commercial
11:41 < MrHindsight> I never joined, yes beer at  https://pumpingstationone.org/
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11:47 < MrHindsight> closest they got to something Bio
11:50 < MrHindsight> https://wiki.pumpingstationone.org/Beer_Church
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11:52 < spurserh> hello
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11:52 < kanzure> be greeted!
11:52 < kanzure> i was describing dna data storage things to spurserh
11:53 < kanzure> and he had some thoughts about radiation write
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11:53 < spurserh> yeah, very interesting stuff. I dunno if my thoughts are valid in any way, was just thinking out loud
11:53 <@fenn> MrHindsight: did analytics lounge go anywhere?
11:54 < spurserh> I was thinking maybe rather than trying to form a tight x-ray beam, one might just guide a tiny particle of radioisotope near the thing one was trying to irradiate
11:54 < spurserh> dose goes with the inverse square of the distance
11:54 < kanzure> i'm really not sure you can do 1 nm beam diameter like this
11:54 < spurserh> 1nm is ambitious
11:55 < kanzure> i think ~1 nm is what you get in dna data storage (ish) (but not per bit..... per bit it's more like 100 nm, since it's statistical or something).
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11:55 < spurserh> the immediate issue that comes to my mind there is, what are you using to track it so precisely
11:56 < spurserh> at 100nm you can use UV light perhaps to track.. there are UV LEDs at 300nm or so
11:56 < spurserh> I was thinking of using a laser diode to get a really small "point source"
11:56 < MrHindsight> fenn: first I've heard of it  :)   I haven't been by there in a year or two
11:57 <@fenn> i saw it mentioned on this page https://wiki.pumpingstationone.org/Vote_to_Donate_SEM
11:58 <@fenn> i sorta wish the "votes" pages had the outcome of the vote on the page
11:58 < MrHindsight> fenn: oh yeah, they moved to a rough part of town
11:58 < MrHindsight> yes, they took the SEM
11:59 < kanzure> is nmz787's SEM working yet
11:59 < kanzure> spurserh: we should have FIB capability soon, one we get the gallium beam running
11:59 < MrHindsight> I think the founder of analytics lounge actually got the SEM for PS1 in the first place
11:59 <@fenn> makes sense
12:00 < spurserh> it seems like the issue is how to make something affordable / scalable, right? I mean, with very expensive machines we can place individual atoms already
12:00 < kanzure> btw, preliminary dna data storage results should be coming in next week (plus/minus holiday hours)
12:00 < spurserh> awesome
12:04 < spurserh> that was pretty quick. the samples were already sent for sequencing?
12:04 < kanzure> submitting them today i think
12:05 < spurserh> wow
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12:05 < spurserh> it seems to me that the read isn't really that hard, but it would consume chemicals just like the write does
12:06 < kanzure> read is nanopore sequencing these days
12:06 < kanzure> http://lab.loman.net/2017/03/09/ultrareads-for-nanopore/
12:07 <@fenn> for degradation based storage methods you need long read lengths
12:08 <@fenn> hmm actually maybe not now that i think about it
12:08 <@fenn> instead of a short repeating sequence you could use a long circular viral genome
12:08 < spurserh> how do you get this nanopore wrapped around the ring?
12:08 < kanzure> "rolling circle amplification" and you have to pick a template with a known sequence
12:08 < kanzure> spurserh: you break the ring
12:09 < kanzure> spurserh: (endo)nuclease enzymes can cut dna molecules
12:09 <@fenn> the circle sequence just repeats endlessly as single stranded dna
12:09 < spurserh> so you cut it and then by chance it will fall into the pore at one end?
12:09 < kanzure> nah it's electrophoretic phenomena
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12:09 < kanzure> so there's a current or something
12:10 < spurserh> you mean, the end of the strand is electrostatically attracted to the pore?
12:10 < spurserh> once cut
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12:10 < kanzure> so,
12:10 <@fenn> it's a flow of ions
12:10 < kanzure> to be more specific, you only need to cut if you are sequencing a circular dna molecule
12:10 < kanzure> otherwise you have linear string shaped molecules
12:10 < spurserh> right, I thought it was a ring in the storage project
12:10 < spurserh> maybe I am behind the times
12:10 < kanzure> ring is template
12:11 < kanzure> polymerase copies a template
12:11 < spurserh> ah, so the written sequence stays linear
12:11 < kanzure> ya
12:11 < spurserh> we don't make a new ring
12:11 < spurserh> I see
12:11 < kanzure> molecular biology quirk in this case...
12:12 < spurserh> and then the end of the linear strand is attracted to the pore electrostatically? or how does it get aligned with the pore?
12:12 < spurserh> physically
12:12 <@fenn> it gets sucked in by the flow of ions (?)
12:12 < spurserh> ah okay
12:12 < kanzure> possibly also helped by law of large numbers in tiny spaces
12:13 < spurserh> so the pore creates a flow of liquid basically
12:13 < kanzure> https://en.wikipedia.org/wiki/Nanopore_sequencing
12:13 < spurserh> yeah I am looking at that
12:14 < spurserh> it doesn't seem to address how they meet up directly
12:14 < spurserh> that's pretty great tho, if it works easily like that
12:15 < gradstudentbot> Does Jesus know about dysprosium?
12:18 < spurserh> looks really cool, you guys have the ability to implement this?
12:20 < kanzure> nanopore sequencing.. hmm.
12:20 < spurserh> I guess this is where the FIB comes in?
12:20 < kanzure> good question. haven't thought about it.
12:20 < kanzure> oh the FIB is just for fun
12:20 < spurserh> nanoscale manufacturing?
12:20 < kanzure> ya
12:20 < spurserh> well, if you don't have a fab, then that seems like how you might do it
12:20 < kanzure> could be useful in this project.... or maybe not.
12:20 < gradstudentbot> Do I have to go through the IRB for that?
12:21 < kanzure> no, gradstudentbot
12:21 < gradstudentbot> Hood life: https://www.facebook.com/photo.php?fbid=296519020495014
12:21 <@fenn> who put facebook urls into it
12:21 < kanzure> :-/
12:21 < spurserh> I am banned from Facebook :(
12:21 < spurserh> cannot view
12:21 < kanzure> doesn't work here either
12:22 < gradstudentbot> I had to remind my professor who I was today.
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12:23 < spurserh> crazy thought: I wonder what the limit is to how small a betatron could be built
12:23 < spurserh> magnetic induction accelerator
12:24 < spurserh> could you make tiny betatrons that make tiny beams and swim around in solution, all producing a pulse of x-rays when a human-scale coil pulses? :-D
12:25 < kanzure> how would you measure success?
12:25 < spurserh> well, you get tiny focused beams of x-rays
12:26 < spurserh> and you don't need tiny wires to the tiny betatrons
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12:26 < spurserh> they are wirelessly powered by the changing magnetic field
12:27 < spurserh> they need an electron source tho.. maybe a spec of radioisotope inside?
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12:27 < spurserh> it's a slightly out-there idea, just a wacky thought that came to me
12:27 < MrHindsight> why DNA for storage? Why not just make your own synthetic polymers that are easily and quickly modified?
12:28 < MrHindsight> choose your shape as well, helix, rings etc
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12:38 < spurserh> isn't it to do with having the nano-machinery for free?
12:38 < spurserh> for copying and cutting and so on
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12:45 < kanzure> spurserh: yes.
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12:54 < spurserh> @kanzure so, if you have a sequence that doesn't transcribe well, like with repetition, can you do some round-about way to copy it? like transcribe to RNA, copy that, and then back to DNA?
12:56 <@fenn> you can design a repeating sequence that doesn't kink or tangle
12:57 < spurserh> I'm wondering if you can mass produce a sequence that won't transcribe well
12:57 < spurserh> by the method used in the actual write cell
12:58 < spurserh> so that your default is that it won't work, and then when you corrupt it, it starts to work (be copy-able)
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13:05 < kanzure> spurserh: copying a repeating strand is OK, it's reading it :-)
13:06 < spurserh> so it's the sequencer that has an issue
13:06 < kanzure> yeah
13:06 < spurserh> I thought you could produce sequences that stopped transcription
13:06 < kanzure> well we're only using a very tiny piece of the transcription infrastructure
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13:06 < spurserh> ah, into RNA
13:07 < spurserh> so, what if you read it by trying to transcribe it into RNA?
13:07 < spurserh> and just measuring if that happened or not
13:07 < spurserh> and perhaps, how much it happened
13:07 < spurserh> https://en.wikipedia.org/wiki/Stop_codon
13:09 < spurserh> or trying to actually make "protein"
13:09 < spurserh> seems nice: you can mass produce it by copying it, and you can see a change of behavior when you corrupt it
13:10 < spurserh> too hard to get that process to happen?
13:10 < kanzure> not sure i understand your stop codon scheme
13:11 < spurserh> it seems that what actually stops is protein synthesis
13:11 < kanzure> polymerase also falls off, can't have it endlessly copying everything
13:11 < spurserh> so start with a ring of stop codons
13:11 < spurserh> no protein is produced
13:11 < spurserh> no precursors consumed
13:11 < kanzure> and you want to modify the ring?
13:12 < spurserh> yeah then when you insert random garbage, you start getting protein synthesis
13:12 < kanzure> and not copy it?
13:12 < kanzure> polymerase doesn't insert though :)
13:12 < spurserh> substitute
13:12 < spurserh> the idea is to "copy" it with garbage substituted in some areas, right?
13:12 < spurserh> that garbage will probably make some protein
13:12 < spurserh> because it substituted for stop codons
13:13 < kanzure> proteins are encoded by a triplet code- only specific 3-letter sequences lead to valid amino acids.
13:13 < spurserh> is it really sparse?
13:13 < spurserh> I thought most codes were valid
13:14 < spurserh> you're substituting lots of triplets, so the probability seems high that you get some protein
13:14 < spurserh> (if it is truly random)
13:15 < kanzure> you can cause polymease to misincorporate but it's random and probabilistic... and you urrently can't cause it to insert a specific 3-letter sequence.
13:15 < spurserh> that seems fine to me
13:15 < kanzure> spurserh: btw you have other proteins you can possibly use http://diyhpl.us/wiki/gene-editing/
13:16 < spurserh> if you're doing, like, 30 triplets at random, isn't the probability of getting no protein very close to 0?
13:16 < kanzure> ya.  but you don't have that specificity here anyway.. you can cause errors but only for stretches of like 100 or 200 bp, lowest resolution.
13:17 < spurserh> right, that's why it could work
13:17 < spurserh> with 100-200 bp randomized, the chances of no protein seem very low
13:17 < spurserh> some stretch will be valid
13:17 < spurserh> maybe there are constraints I don't know, like minimum length of a valid stretch
13:18 < spurserh> all that matters is that some protein is made, not what protein
13:19 < spurserh> 0 = no protein synthesis, 1 = some measurable synthesis
13:20 < spurserh> default being 0
13:20 < spurserh> a ring of stop codons
13:20 < spurserh> this assumes that coding triplets are a dense set, and non-coding / stop codons are sparse
13:20 < kanzure> it's not 100 randomized. it's 100 bp but unknown amount are randomized.
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13:21 < spurserh> unknown amount? as in +- 10?
13:21 < kanzure> ya
13:21 < spurserh> it's a continuous stretch of randomized ones on the order of 100 right?
13:21 < spurserh> so that's fine
13:21 < kanzure> could be 20... could be 10... etc.
13:21 < spurserh> I'm thinking of this probabilistically
13:21 < spurserh> no need to be precise
13:22 < spurserh> what matters is that the highest possible chance of no valid stretch is below some threshold
13:22 < spurserh> and then you design the error correction software on top of that
13:25 < kanzure> yeah i need to figure out the error correction approach
13:26 < spurserh> my idea is that you can detect easily if any protein synthesis has occurred
13:26 < spurserh> so you don't have to sequence anything
13:26 < spurserh> maybe you measure consumption of precursors, for instance
13:27 < spurserh> sequencing is overkill, you're sequencing random noise
13:27 < kanzure> yes one common lab technique is gfp (fluorescence) (a protein)
13:27 < kanzure> so if it glows / no glows
13:27 < spurserh> but that requires a certain sequence right?
13:28 < spurserh> you could separately try to make gfp, and if the precursors are exhausted on garbage proteins, then it won't synthesize
13:28 < spurserh> so, your default "stop codon ring" gives you a glow
13:28 < spurserh> the randomized ring does not
13:30 < spurserh> but hey, that reminds me of an even simpler idea: have a ring of a certain proportion of precursors. the randomized ring takes a different proportion to copy
13:30 < spurserh> test whether or not a particular precursor was exhausted first
13:32 < spurserh> is it easy to detect a particular pyrimidine in solution?
13:32 < spurserh> my mind immediately goes to radioactive pyrimidines :-p
13:32 < kanzure> spectroscopy.. stuff.
13:32 < spurserh> if spectroscopy can be done cheaply in a memory cell..
13:33 < spurserh> well, if you can make proteins, why not make transcriptase
13:33 < spurserh> your default ring codes for transcriptase
13:33 < spurserh> creating an exponential chain reaction
13:33 < spurserh> the corrupted ring does not
13:34 < spurserh> :-D
13:34 < spurserh> but yeah, a ring coding for gfp seems like the simplest way to go doesn't it? when it's corrupted, the result doesn't glow
13:35 < spurserh> that one is actually a serious idea
13:38 < kanzure> for testing? sure.
13:39 < spurserh> what limits it from automated use as a reading mechanism?
13:40 < spurserh> there is even self-destructing gfp https://www.researchgate.net/publication/13680059_New_Unstable_Variants_of_Green_Fluorescent_Protein_for_Studies_of_Transient_Gene_Expression_in_Bacteria
13:43 < spurserh> if there is only one linear strand (modified copy), then as it is translated over and over into protein, there should be discrete increases in the light output
13:44 < spurserh> it might need a photomultiplier to detect tho, again perhaps not practical at scale
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13:45 < kanzure> what did you want to read though?
13:46 < spurserh> the bits that were written
13:46 < kanzure> and use gfp for that?
13:46 < kanzure> there was a recent paper about using mass spectrometry for reading data https://www.nature.com/articles/s41467-017-01104-3
13:47 < spurserh> yeah, if you have your UV light on, and a sensitive detector of photons in the fluorescence range, then as the linear strand gets transcribed, you'll get a pulse signal
13:47 < spurserh> the photon count will increase in discrete steps as gfbs are created
13:47 < spurserh> a ring could make 0 - 10 gfbs, let's say
13:47 < spurserh> so that's 11 bits
13:48 < kanzure> there's a way to generate fluorescence called sequencing by synthesis
13:48 < kanzure> .wik sequencing by synthesis
13:48 < yoleaux> "Illumina dye sequencing is a technique used to determine the series of base pairs in DNA, also known as DNA sequencing. The reversible terminated chemistry concept was invented by Bruno Canard and Simon Sarfati at the Pasteur Institute in Paris." — https://en.wikipedia.org/wiki/Sequencing_by_synthesis
13:48 < kanzure> hm no
13:48 < spurserh> our case is much simpler tho
13:49 < spurserh> we don't care what the sequence is, just if it has been randomized or not
13:49 < spurserh> so the original sequence can just be gfb,gfb,gfb,gfb
13:49 < spurserh> 0,0,0,0
13:49 < spurserh> and if we want to write a 1, we put garbage
13:50 < spurserh> gfb,gfb,asd,gfb
13:50 < kanzure> no that's not how you use fluorescence in dna sequencing
13:50 < spurserh> we aren't trying to do dna sequencing
13:50 < spurserh> we are trying to store and read bits
13:50 < kanzure> .wik Single molecule real time sequencing
13:51 < yoleaux> "Single molecule real time sequencing (SMRT) is a parallelized single molecule DNA sequencing method. Single molecule real time sequencing utilizes a zero-mode waveguide (ZMW)." — https://en.wikipedia.org/wiki/Single_molecule_real_time_sequencing
13:51 < kanzure> ah here we go,
13:51 < kanzure> the pacbio people
13:51 < kanzure> http://diyhpl.us/~bryan/papers2/bio/Real-time%20DNA%20sequencing%20from%20single%20polymerase%20molecules.pdf
13:52 < spurserh> that is very cool, but seems far more complicated
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13:54 < spurserh> shows that you can detect such tiny pulses tho
13:54 < spurserh> here is the important question: do you care what the codons are?
13:54 < spurserh> my impression was that the only thing being detected, finally, was "changed or unchanged"
13:55 < kanzure> codons are only useful for protein synthesis
13:55 < spurserh> right, so you don't care
13:55 < spurserh> so they can be anything
13:55 < spurserh> so why can't they be the code for gfb?
13:56 < kanzure> seems like you want gfp fluorescence to code for data. instead of direct nanopore sequencing of the data storage molecules.
13:56 < spurserh> yes
13:56 < kanzure> i think the problem here is order
13:56 < spurserh> the ordering is by time
13:56 < spurserh> there is a certain translation rate, right?
13:56 < gradstudentbot> Don't disturb me. I'm reorganizing my slide collection.
13:56 < kanzure> not sure that would work, but interesting to try sometime.
13:57 < spurserh> I am certainly not sure either :)
13:57 < spurserh> what I am most unsure about is if a detector cheap and simple enough to go into a memory cell can be sensitive enough
13:58 < spurserh> I think with a big/expensive photomultiplier it can work
13:58 < spurserh> the principle could be tried just with a printed ring right, with some gfb segments and some randomized segments
13:58 < spurserh> let it translate and see how the pulses look
13:59 < spurserh> (sorry, by printed, I mean synthesized)
13:59 < gradstudentbot> Protip: don't trust random pipette tips laying around.
13:59 < gradstudentbot> I am sponsored by New England Biolabs.
13:59 < spurserh> ah, it really is a bot
13:59 < spurserh> hmm, there are different flavors of gfb, right? different colors
14:00 < spurserh> that could encode the sequence
14:00 < spurserh> red green blue red green blue red green blue
14:00 < spurserh> that can help synchronization and increase information density
14:00 < spurserh> translation would proceed at different speeds for lots of reasons
14:01 < spurserh> temperature, availability of precursors, etc, right?
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14:08 < spurserh> huh.. the proportions of those colors could be the whole message. then you don't need to detect tiny pulses at all
14:08 < spurserh> you let it run away and synthesize gazillions of gfbs of various colors, like you would for testing in the lab normally
14:09 < spurserh> then you just look at what proportion you end up with
14:09 < spurserh> which is easy with ordinary photodiodes
14:09 < spurserh> (you start with equal proportions, say, and you "knock out" gfbs from the sequence when you write)
14:10 < spurserh> so if it goes rgbrgbrgbrgb, and I knock out every 3rd, I will lose one color..
14:10 < spurserh> but maybe it doesn't stay nicely in sync like that, so the pattern of knock-outs will be more complex, but an algorithm should be able to solve it
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14:13 < spurserh> maybe not, if the copying rate is too variable
14:13 < spurserh> on the write
14:13 < spurserh> how tightly can that be controlled? the copy rate? you said it is +- 20% @kanzure?
14:14 < kanzure> yes there is rfp not just gfp
14:15 < kanzure> uh not really sure yet
14:17 < spurserh> basically drift will reduce our number of colors. so with 10% drift per write, and each write being one gfb for simplicity, and 8 colors total, we go down to 4 colors with a sequence of bits that's >5 long
14:18 < spurserh> so that's 6 levels of 4 colors, or 4096 possibilities
14:18 < spurserh> 12 bits
14:19 < spurserh> 12 bits in 300 bases per gfb * 5 = 1500 bases
14:19 < spurserh> that's pretty good isn't it?
14:19 < spurserh> and we can read it using a photodiode and an LED
14:20 < spurserh> that's assuming 10% drift per write, 8 colors (varieties of gfb), and 1 write = 1 gfb length
14:21 < spurserh> *gfp
14:21 < spurserh> I got the idea from this image https://en.wikipedia.org/wiki/Green_fluorescent_protein#/media/File:FPbeachTsien.jpg
14:23 < spurserh> sorry, 8 photodiodes, and 8 LEDs, I suppose
14:23 < spurserh> up to that, max
14:23 < spurserh> (will take minutes to read I suppose)
14:23 < spurserh> (but you could just keep it in a "ready-ready" state)
14:24 < spurserh> (write to read latency is minutes, but after that it can be read in microseconds any time)
14:24 < spurserh> *read-ready
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14:51 < spurserh> can add non-coding filler gaps to conserve all the colors, too, further increasing the information density
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14:53 < kanzure> back hi
14:54 < kanzure> yes it's something to consider
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14:55 < spurserh> would there be multiple different written linear strands per cell?
14:55 < MrHindsight> lotsa bases for so little data
14:55 < spurserh> or 1 write per cell?
14:55 < spurserh> it's higher density than what I was told about..
14:56 < spurserh> the write is 1 bit per 100 bases max, right @kanzure?
14:56 < MrHindsight> I wonder what they really want the DNA synthesis for
14:57 < spurserh> dna synthesis? they?
14:57 < MrHindsight> DNA as media for memory
14:57 < spurserh> well, it's not dna synthesis
14:58 < spurserh> it's scrambling 100 base regions
14:58 < spurserh> isn't it @kanzure?
15:03 < kanzure> this technique does ot use chemical dna synthesis, it uses enzymatic dna synthesis
15:03 < kanzure> *does not
15:04 < MrHindsight> heh, chemical free enzymes
15:04 < kanzure> chemical synthesis is something much different
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15:10 < spurserh> oops
15:10 < spurserh> ignore that
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15:31 < maaku> kanzure: well presumably they'd only be selling a portion, retaining founder-like ownership of the remaining amount
15:48 < nmz787> kanzure: not yet, I haven't really worked on the chiller/cooler unit in a few months... been working on the DNA stuff and the electroporator
15:50 < kanzure> alright
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16:18 < kanzure> .title https://www.youtube.com/watch?v=XNhKNip1cJk
16:18 < yoleaux> Ultrasound pulse and receive using OpenUltrasound PCB and common piezo discs - YouTube
16:19 < spurserh> I am thinking of using a raw TFT for the first prototype now, rather than USB
16:19 < spurserh> just less hassle
16:19 < kanzure> .title https://arxiv.org/abs/1611.10174
16:19 < yoleaux> [1611.10174] A low-cost, arduino-like dev-kit for single-element ultrasound imaging
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16:21 < spurserh> this is Murgen right?
16:22 < kanzure> ah yes
16:22 < kanzure> yes that one
16:23 < spurserh> are those the same guys as this ? http://www.opensourceimaging.org/project/echopen/
16:23 < kanzure> no i think that's different people, or something
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17:32 < nmz787> spurserh: TFT for a display?
17:32 < spurserh> yeah
17:32 < spurserh> parallel RGB interface, just easy to get working
17:32 < spurserh> can add the USB data out later
17:33 < nmz787> I just got some small I2C displays
17:33 < nmz787> super easy
17:33 < nmz787> I don't need high-refresh though
17:33 < spurserh> yeah, these are even easier, literally 24 lines for RGB
17:33 < spurserh> and then a clock and it reads a pixel on posedge
17:33 < nmz787> I2C is 2 wires
17:33 < spurserh> yeah, low refresh on i2c because it's slow
17:33 < spurserh> the parallel interface is fast
17:33 < spurserh> but you need lots of IO (I am using an FPGA)
17:34 < nmz787> .wik prolactin
17:34 < yoleaux> "Prolactin (PRL), also known as luteotropic hormone or luteotropin, is a protein that is best known for its role in enabling mammals, usually females, to produce milk. It is influential in over 300 separate processes in various vertebrates, including humans." — https://en.wikipedia.org/wiki/Prolactin
17:34 < nmz787> spurserh: word
17:34 < spurserh> a lot of those i2c displays will also support SPI, should give a much higher datarate
17:35 < nmz787> I do systemverilog programming at work, but am no means an expert or even very good at it... and I only work on the testbench stuff
17:35 < spurserh> I'm fairly new to it as well. at work I use Catapult HLS
17:35 < spurserh> only recently started dipping into the Verilog
17:36 < spurserh> it's an exciting time to learn FPGAs tho www.clifford.at/icestorm/
17:36 < nmz787> I honestly like hardware better than C/C++... but pretty much love Python
17:37 < nmz787> yeah
17:37 < nmz787> I think I've got an ice40 around here
17:37 < nmz787> I've got a de0-nano too
17:37 < spurserh> icestorm is easy to set up
17:37 < spurserh> and really works well
17:37 < nmz787> programmed it to blink once using a Python to HDL converter which also automated the build and programming toolchain flow ;)
17:37 < spurserh> hehe
17:38 < spurserh> icestorm comes with some good blinky examples
17:38 < nmz787> so I basically ran a single command and 10+ mins later it was blinking
17:38 < spurserh> there's something called IceStudio now https://github.com/FPGAwars/icestudio
17:38 < spurserh> and an Arduino-like board too https://github.com/FPGAwars/icezum/wiki
17:38 < spurserh> there are even some soft AVR cores that can run Arduino programs
17:38 < spurserh> the barriers are falling fast
17:39 < nmz787> indeed
17:39 < nmz787> I have been using MicroPython lately
17:40 < nmz787> got some ADC and DMA stuff hacked together in the underlying C which I can call from the Python interface
17:40 < nmz787> I connect the USB cable and it shows up as a storage media device and COM port at the same time
17:40 < spurserh> cool, I didn't know about that
17:41 < nmz787> you get a Python terminal on the serial port, and saving a file on the media-device along with a CTRL-D on the terminal will refresh the "filesystem" with your latest changes
17:42 < nmz787> you can have it run code on boot, etc
17:43 < nmz787> pretty nifty for products targeting non-programmers
17:43 < nmz787> or newbs
17:43 < gradstudentbot> Wasn't that a Nature paper?
17:43 < nmz787> basically
17:43 < spurserh> compiler on the micro, reminds me of nodemcu
17:43 < spurserh> yeah
17:44 < gradstudentbot> Who used the last of the buffer?
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18:15 < kanzure> yashgaroth: nate wants prosthetic mammaries, you got anything for that?
18:16 < yashgaroth> like thorazine or
18:16 < kanzure> well i told him use a prosthetic implnt
18:16 < kanzure> implant
18:16 < kanzure> instead of overdosing on prolactin
18:17 < nmz787> for lactation
18:17 < yashgaroth> a...bottle?
18:17 < nmz787> I was thinking the Odin's self-mod kit with a prolactin gene thrown in
18:18 < kanzure> no way prolactin is enough
18:19 < nmz787> .wik https://en.wikipedia.org/wiki/Male_lactation#Human_male_lactation
18:19 < yoleaux> nmz787: Sorry, that command (.wik) crashed.
18:19 < nmz787> .wik Male_lactation#Human_male_lactation
18:19 < yoleaux> nmz787: Sorry, that command (.wik) crashed.
18:19 < nmz787> hope you humans can figure it out...
18:20 < yashgaroth> not to interrupt this, but kanzure did you hear about that dodo omnidata company from jojack? seeing as how they're based out of BTNB
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18:20 < kanzure> yashgaroth: nmz787 and i met them at the dna data storage workshop
18:21 < kanzure> DataPacRat: hi we build self-replicators in here
18:21 < yashgaroth> ah, I checked their site and the address is jojack's lab so he may know more
18:21 < kanzure> DataPacRat: search your inbox for my email yo
18:21 < kanzure> it was from 2014
18:21 < kanzure> yashgaroth: ah i didn't know that. shit.
18:21 < DataPacRat> ... I'm still getting used to a being active in one chatroom at a time; pardon me if I make blunders getting used to more than one.
18:21 < kanzure> yashgaroth: i haven't figured out what they are doing
18:22 < kanzure> yashgaroth: jojack mentioned something to me about dna data storage, didn't know it was them, thanks
18:22 < yashgaroth> yeah it's pretty vague and I couldn't find any relevant patents from them
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18:22 < DataPacRat> kanzure: You sent it from your username at gmail?
18:23 < kanzure> DataPacRat: correct
18:23 < gradstudentbot> Yeah, it's significant.
18:24 < kanzure> yashgaroth: thanks, just sent an email about that, much 'ppreciated & so on
18:24 < yashgaroth> np
18:25 < DataPacRat> kanzure: Found it. ... RL is currently somewhat busy and distracting (family stuff), so if you don't mind, I'll put it in a fresh tab to pay better attention to when I'm more solitary.
18:25 < kanzure> DataPacRat: okay sure
18:26 < DataPacRat> It's been a few years; I suspect a few extra hours aren't much of a social faux pas. :)
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18:26 < kanzure> DataPacRat: yeah could be worse
18:27 < DataPacRat> That said... uh, hi everyone; I'm a cryonicist with a habit of writing 90% of novels, and may have recently cured my depression by keeping my brain's oxygen from dropping to 80% every night.
18:27 < kanzure> we have a few cryonics people
18:28 -!- yashgaroth [~yashgarot@2606:6000:cd4d:3300:f5e0:f867:a11d:8d52] has quit [Ping timeout: 240 seconds]
18:30 < DataPacRat> I'm also getting ready to write a novel based on "the last person in the universe", an em waking on Phobos with a rocket and a factory-in-a-box. I'm about to heavily revamp the previous outline at https://docs.google.com/document/d/1XcgNwELHCU-r7GuYUgDNDDIviThd8Y7Bdto_kMIcmlI/edit , but would still appreciate any constructive criticism.
18:33 < kanzure> DataPacRat: cells are self-replicators
18:34 < nmz787> yashgaroth_: yeah I think I mentioned before in here that they were working out of there
18:34 < kanzure> ah hell. sorry man, i missed that.
18:35 < DataPacRat> kanzure: Okay...
18:35 < kanzure> DataPacRat: well it turns out hardware is hard.. and if you want molecular nanotechnology self-replicators, that's called biology.
18:36 < DataPacRat> kanzure: Nope, going for old-style clanking-replicators.
18:36 < kanzure> do you have any thoughts on how to build one?
18:36 < DataPacRat> I'll be digging up "Advanced Automation for Space Missions" for some inspiration.
18:36 < DataPacRat> And probably stealing some of the manufacturing techniques described in the board game "High Frontier" for further inspiration.
18:36 < kanzure> unfortunately a design was not proposed in AASM
18:37 < nmz787> 2017-09-14.log:16:50 < nmz787> kanzure: dodo's lab is out of biotechnbeyond
18:37 < kanzure> oh weren't we busy that day
18:38 < DataPacRat> The main relevant handwave I'll be using was that a bunch of humans on Earth worked out a lot of bugs in the basics of such a system, and my protagonist inherited the relevant data.
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19:01 < kanzure> DataPacRat: have you read orionsarm.com ?
19:02 < kanzure> fixedzero: hi
19:02 < DataPacRat> kanzure: http://www.orionsarm.com/eg-article/4ba1012793821 :)
19:02 < nmz787> .title
19:02 < yoleaux> Orion's Arm - Encyclopedia Galactica - '_____' Spores
19:04 < fixedzero> kanzure: hi :)
19:04 < kanzure> fixedzero: what brings you this way
19:05 < fixedzero> back on IRC after many moons away, trying to find some channels that interest me
19:06 <@fenn> .wik autofac
19:06 < yoleaux> ""Autofac" is a 1955 science fiction short story (part of the collection Robots, Androids, and Mechanical Oddities published in 1984) by Philip K. Dick that features one of the earliest treatments (and Dick's second) of self-replicating machines." — https://en.wikipedia.org/wiki/Autofac
19:06 < kanzure> fixedzero: we are implement things http://diyhpl.us/wiki/hplusroadmap
19:06 < fixedzero> merci
19:06 < fixedzero> reading now
19:07 < kanzure> 19:06 < DataPacRat> https://www.google.ca/search?q=rat+brain+implant+human+organoids
19:12 < DataPacRat> Possibly related to this channel: While I'm on a fixed income, I'm thinking of looking for inexpensive St. John's Wort, due to http://www.informationisbeautiful.net/visualizations/snake-oil-scientific-evidence-for-nutritional-supplements-vizsweet/ ; and possible other items near that chart's tops. Anyone care to offer suggestions or advice?
19:12 < kanzure> aliexpress. buy in bulk.
19:13 <@fenn> http://www.sfherb.com/St-Johns-Wort-Cut--1-Lb_p_354.html or swansonvitamins.com
19:13 < DataPacRat> kanzure: ... Heard of it, but last time I visited, everything I browsed required ridiculously large orders. ... Though that was a while ago.
19:13 < DataPacRat> (Am in Canada, if that's relevant for shipping.)
19:13 < kanzure> well how long do you plan on living?
19:14 < DataPacRat> kanzure: At least 13 more years; more than that would be gravy.
19:16 < DataPacRat> (Looking at sfherb) ... How long does St. John's Wort last? How fast does 5 lbs of the stuff get /used/?
19:16 <@fenn> no idea
19:17 <@fenn> SSRI's are stupid
19:17 <@fenn> i mean if it works for you, great, but you have a 1/5 chance of it actually helping
19:18 <@fenn> (st john's wort is an SSRI, if that wasn't obvious)
19:19 < DataPacRat> fenn: So a better approach might be to try a small/cheap initial sample, to find out if bulk might be worth looking into?
19:20 <@fenn> ah my bad, sfherb has a $30 minimum order now
19:25 <@fenn> "It acts as a reuptake inhibitor of monoamines, including serotonin, norepinephrine, dopamine, and of GABA and glutamate"
19:26 <@fenn> hrmmm
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19:33 <@fenn> forget what i said earlier, it's not an SSRI
19:39 <@fenn> make sure you avoid anything on this list of drug interactions while taking it https://en.wikipedia.org/wiki/St._John%27s_wort#Pharmacodynamic
19:42 < DataPacRat> fenn: Thanks for the warning. Good news, I don't touch any of those items.
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19:48 < kanzure> fenn: https://www.fastcompany.com/3013789/my-quest-to-create-self-building-self-tooling-people-free-manufacturing-plants
19:50 < kanzure> or i guess it's this one https://www.seed-factory.org/
19:50 < kanzure> actually it's not clear to me if i am still conflating you two people
19:50 <@fenn> i am not dani eeder
19:51 <@fenn> the dread god eder
19:51 < kanzure> no i think it's DataPacRat
19:51 < DataPacRat> I have no idea what "eeder" or "eder" are.
19:51 < kanzure> hmm
19:51 < kanzure> so you both want autonomous self-replicating factories?
19:51 < kanzure> and you both posted to sl4?
19:52 < DataPacRat> I have an interest in Von Neumanning, but "sl4" isn't ringing a bell.
19:52 < kanzure> from 2011 http://sl4.org/archive/1106/21168.html
19:53 < kanzure> ok
19:53 < kanzure> well anyway, i was wrong about this.
19:53 < DataPacRat> I will admit that I'm the one and only DataPacRat, so that was posted by me. (Reads what was actually posted.)
19:53 < kanzure> https://www.seed-factory.org/contributing-members/
19:53 < kanzure> and i am pretty sure you are both bitcoin users
19:54 < DataPacRat> I technically have a Bitcoin wallet, though I haven't actually run the program in... years, by now.
19:54 < DataPacRat> And given I was born in '76, I'm pretty sure I wasn't working for Boeing in '81. :)
19:54 < kanzure> easy for me to make this kind of mistake
19:54 < kanzure> womp womp
19:55 < kanzure> i mean there's only a handful of people working on self-replication anyway :-)
19:55 < DataPacRat> No worries.
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19:55 < DataPacRat> I'm entirely an interested amateur, at this point.
19:55 <@fenn> are you now or have you ever been a member of the organization known as '___'
19:56 < DataPacRat> fenn: It was one of my early explorations of self-replication.
19:56 < DataPacRat> (... I still like the pictures of the '_____'s, now that I'm looking at them.)
19:57 <@fenn> cute bushbot tail
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19:59 < gradstudentbot> I think using the laser is making me sterile.
20:00 <@fenn> this was the original: http://fennetic.net/irc/christmas-bush http://fennetic.net/irc/christmas-bush.png
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20:58 < nmz787> wasn't there a link posted in here recently about the massive number of unreplicatable papers?
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--- Log closed Sat Nov 18 00:00:18 2017