--- Log opened Sun Jan 14 00:00:23 2018
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04:15 < maaku> drexlarian nanotube based computational elements is the only thing I can think of that would use this mechanical computational gate design competatively with electronic gates but that seems a little far away?
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06:32 < juul> ok i just looked at the planaria memory article. that is fucking crazy
06:33 < juul> i didn't read the whole thing. is it possible that memories are just being stored in neural structure outside of the brain? or is it definitely using a completely different memory-storage mechanism?
06:33 < kanzure> they re-trained the worms after regeneration
06:48 < juul> yeah but they still outperformed the untrained worms even though those were also retrained (well for them it was the first training)
06:48 < juul> but i do see a potential issue with the protocol
06:48 < juul> they just threw away any worms that completely failed to reach the food in 60 mins
06:49 < juul> and they don't specify how many failed out of the total
06:49 < juul> it is likely that the number of failed decapitated is higher than the number of failed non-decapitated
06:50 < juul> so without more data it's impossible to tell if they're simply getting rid of worms with a lower general fitness for that environment by chopping their heads off and only keeping the ones that are sane enough to find food in under 60 mins after regrowing their heads
06:56 < kanzure> ah a selection effect
06:56 < kanzure> or they are just picking the lucky ones that wormed their way to the food anyway
06:57 < juul> perhaps
06:58 < juul> from the same author which cites the paper: http://onlinelibrary.wiley.com/doi/10.1113/jphysiol.2014.271940/full
07:00 < juul> so you can make these things have two heads if you slice them just right and let them regrow
07:00 < juul> and they often reproduce via fission
07:00 < juul> and then to support his theory about the bioelectric memory he says: "Although there are no data suggesting that this 2-head phenotype persists through sexual reproduction, it is in fact inherited across these animals’ most frequent natural mode of reproduction: fission."
07:01 < juul> yeah... that's not really super surprising is it?
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07:02 < Jenda`> juul: I don't find it crazy that simple organisms store the information across the entire NS
07:03 < Jenda`> ofc this is not the case of humans, as demonstrated e.g. by spinal cord injury in the neck - such person seems to remembed everything and can communicate normally with eyeblinks etc.
07:04 < juul> Jenda`: yeah that sounds fine. he's proposing that it is being stored in non-neuronal cells using bioelectric mechanisms
07:04 < juul> that also sounds plausible
07:05 < juul> though how transfer of memories between brain cells and these non-neuronal cells occurs i can't imagine
07:07 < juul> but his reasoning that a physical modification to the organism being inherited through fission is somehow evidence of this... that is a huge stretch
07:08 < juul> most of differentiation is guided by biochemical/genetic mechanisms
07:08 < juul> modifying the organism through surgery modifies the biochemical gradients
07:09 < juul> that those biochemical gradient changes persist after fission is really not super surprising
07:15 < juul> it also seems to me that they appear to be proposing an entire new field at the level of importance of epigenetics, with regards to bioelectric signalling
07:16 < juul> but isn't what he's talking about simply ion gradients? which most people would see as a subset of chemical gradients?
07:17 < juul> "The gradients are produced by genes encoding ion channels and pumps, and regulate expression of numerous downstream target genes"
07:18 < juul> yeah... this looks like someone fishing for funding by way of rebranding
07:18 < juul> but if this non-neuronal memory is a real phenomenon, and they can figure it out, then hey whatever works
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08:40 < kanzure> https://en.wikipedia.org/wiki/Template:Kinases
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09:51 < kanzure> juul: do you know twist's cost per wash step? or cost per reaction? they claim their cost per bp is $1e-12/base  but i don't know if this includes their wash step costs per base..
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10:00 < kanzure> http://www.chromatographyonline.com/continuing-acetonitrile-shortage-how-combat-it-or-live-it
10:01 < kanzure> (from 2009 obviously, when acetonitrile prices spiked due to supply shortage)
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10:41 < kanzure> http://www.glenresearch.com/Catalog/contents.php
10:42 < kanzure> http://www.glenresearch.com/Catalog/Catalog2017_02.pdf
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11:02 < kanzure> twist's reaction volume is 100 nanoliters per spot https://cen.acs.org/articles/93/i43/Twist-Bioscience.html
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11:36 < kanzure> "Another approach to error correction uses SURVEYOR endonuclease (Transgenomic), a mismatch-specific DNA endonuclease to scan for known and unknown mutations and polymorphisms in heteroduplex DNA. SURVEYOR technology is based on a mismatch-specific DNA endonuclease from celery, Surveyor nuclease, which is a member of the CEL nuclease family of plant DNA endonucleases (Qiu et al., 2004). ...
11:36 < kanzure> ...Surveyor nuclease cleaves with high specificity at the 3′ side of any base-substitution mismatch and other distortion site in both DNA strands, including all base substitutions and insertion/deletions up to at least 12 nucleotides. Insertion/deletion mismatches and all base-substitution mismatches can be recognized, with varying efficiency of cleavage based on the mismatch sequence. In one ...
11:36 < kanzure> ...example, Surveyor nuclease technology can be used for mismatch detection in a method involving four steps: (i) optional polynucleotide amplification, e.g. PCR, of desired polynucleotide targets with both mutant/variant and wild-type/desired sequences; (ii) hybridization resulting heteroduplexes comprising mismatches; (iii) treatment of heteroduplexes with Surveyor nuclease to cleave at ...
11:36 < kanzure> ...mismatch sites; and (iv) optional analysis of digested polynucleotide products using the detection/separation platform of choice (FIGS. 15-16)."
11:43 < kanzure> https://patents.google.com/patent/US20170095785A1/en
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13:33 < kanzure> https://www.src.org/program/grc/semisynbio/semisynbio-consortium-roadmap/6043-full-report-dna-based-storage-final-twg1.pdf
13:33 < kanzure> in this document, twist claims a cost of $1e-12/bp
13:40 < kanzure> fenn: for precise positioning of an inkjet printhead (e.g. after movement), can inserting/removing multiple screws be sufficient to align everything again to some surface? or will a tight fit still be misaligned compared to original alignment?
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15:16 < kanzure> "Systems of mechanized and reactive droplets powered by multi-responsive surfactants" https://www.nature.com/articles/nature25137n
15:17 < kanzure> "Here we describe surfactants based on functionalized nanoparticle dimers that combine all of these and several other characteristics. These surfactants and therefore the droplets that they cover are simultaneously addressable by magnetic, optical and electric fields. As a result, the surfactant-covered droplets can be assembled into various hierarchical structures, including dynamic ones, in ...
15:17 < kanzure> ...which light powers the rapid rotation of the droplets. Such rotating droplets can transfer mechanical torques to their non-nearest neighbours, thus acting like systems of mechanical gears. Furthermore, droplets of different types can be merged by applying electric fields and, owing to interfacial jamming11,12, can form complex, non-spherical, ‘patchy’ structures with different surface ...
15:18 < kanzure> ...regions covered with different surfactants. In systems of droplets that carry different chemicals, combinations of multiple stimuli can be used to control the orientations of the droplets, inter-droplet transport, mixing of contents and, ultimately, sequences of chemical reactions. "
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15:26 < kanzure> http://www.spherefluidics.com/technology/
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15:55 < kanzure> https://patents.google.com/patent/US20070172837A1
15:58 < kanzure> .title https://www.youtube.com/watch?v=YcxzDxIT358
15:58 < yoleaux> Ink Jet Discharge - YouTube
16:01 < kanzure> .ttle https://www.youtube.com/watch?v=XfrsaV0dfDE
16:02 < kanzure> .title https://www.youtube.com/watch?v=EVYmQiRCR_U
16:02 < yoleaux> The drip printer in action - YouTube
16:13 < kanzure> .title https://www.youtube.com/watch?v=gbKWcD2xfbI
16:13 < yoleaux> 22khz ultrasonic transducer atomizing water - YouTube
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17:24 < fenn> screws are not a good alignment method, as they require a bit of slop to work at all. but you could maybe add a couple dowel pins and matching holes
17:26 < fenn> for micron precision alignment you'd want to use a kinematic mount
17:28 < fenn> https://practicalprecision.com/kinematic-constraint/
17:30 < fenn> if you ever remove the head from this mounting plate you have to recalibrate its position relative to the machine frame
17:32 < kanzure> some amount of slop is fine as long as it's... averaging around an exact point.
17:32 < fenn> it could be off by as much as 500 microns if you have to take out the screws
17:32 < kanzure> oh.
17:32 < kanzure> i want more like, off by 10 microns
17:33 < fenn> might be doable with dowels
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17:33 < kanzure> every time i look at twist's stuff i keep thinking that they are doing some sort of alignment and screwing to create a seal at their interface
17:50 < kanzure> streptavidin-biotin binding strength is like 50 piconewtons http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0188722   is that right?
17:52 < kanzure> "different force loading rates, we obtained narrow force distributions of the bond rupture forces ranging from 200 pN at 1,500 pN/s to 230 pN at 110,000 pN/s" what?
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19:06 < juul> what?! $0.00000000001 per bp? biobricks foundation is getting ripped off :p
19:13 < kanzure> well that's not a price it's a cost
19:14 < kanzure> according to their cto in 2016 during a workshop, $1e-12/bp is a cost they have....... now whether that's per cycle or just phosphoramidites or something... hard to tell.
19:14 < juul> yeah it's kinda a silly number given "however, in practice, this number would be much higher due to the additional cost of constructing, operating and maintaining 1,000 synthesis machines."
19:15 < juul> so what is that cost? just the cost of consumables and electricity? does it include worker salaries? (i'd assume not)
19:15 < kanzure> well also, if they have $1e-12/bp true cost per cycle then i think the synthetic biology market would be... 10000x bigger right now.
19:15 < juul> yes
19:15 < kanzure> my best guess is that it's only some of the consumables, like the phosphoramidites
19:15 < kanzure> twist says they use only 100 nanoliters per reaction... but for acetonitrile that's still $25 per bp (over a million spots) so $600 per chip (1.6 million oligos)
19:16 < juul> yeah. that's like saying that CPUs should be dirt cheap because sand is cheap
19:16 < kanzure> (1 oligo = 150 bp on their chips)
19:16 < kanzure> so i have been given other numbers, to make this even more confusing
19:16 < kanzure> the $1e-12/bp number is from 2016
19:17 < kanzure> in 2017 i heard from their cto at another workshop that it's $0.0001/bp
19:17 < kanzure> and $25k for a full chip
19:17 < kanzure> no idea if this includes quality assurance costs, sequencing, etc... no clue.
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19:18 < kanzure> and, finally, i have heard that their *price* is about $0.03/bp  and on their website they advertise more like $0.07 or $0.09 per "gene" which includes lots of quality assurance and other stuff...
19:18 < kanzure> oops sorry i mean $0.07 per bp in a "gene"
19:18 < juul> well, i can't remember the price BBF is getting, nor if it's supposed to be secret, but I think it's no more than 3 cents per bp and that does definitely not include any quality assurance other than that I think they may try to make it twice before deciding that it won't work
19:19 < juul> and no sequencing
19:19 < kanzure> waiiit what... no sequencing?
19:20 < kanzure> i think $0.03/bp is really high if they aren't doing sequencing.... because they claim to have optimized everything down to really small volumes..
19:20 < juul> i'm going down to stanford on friday and will ask if it's ok to share precise numbers publicly
19:20 < kanzure> how do they deliver their dna? if you ask for 500 sequences, how do you get the 500 different materials back in the mail? what form factor
19:21 < juul> i believe we get it in 96-well plates but i haven't actually been in the lab since we got our first delivery
19:21 < juul> but i can share some more details friday
19:21 < kanzure> so each well has a different dna
19:21 < kanzure> and ideally all the molecules are homopolymers inside each well
19:23 < juul> i believe bbf gets sequences of up to 1850 bp and then do the cloning to combine longer sequences and insert into plasmids using an opentrons
19:23 < juul> there's a sequencing step after the cloning
19:23 < kanzure> i think twist does some assembly steps to get 1850 bp...
19:23 < kanzure> no way they are cranking out 1850 bp oligos from phosphoramidite chemistry
19:24 < juul> yeah unlikely. but we got a deal from them that had some gotchas to keep the price low
19:24 < juul> their IT integration also really needs work
19:25 < juul> but no-one else could compete with their pricing
19:25 < juul> we're using separate companies for synthesis, sequencing and third party rights checking
19:25 < kanzure> alright well in the mean time have fun: docker -H docker.twistbioscience-staging.com ps
19:26 < kanzure> i think some of their numbers must be lies
19:27 < kanzure> $0.0001/bp is competitive with other array synthesis tech... but twist has, supposedly, spent some time optimizing their setup.... but $1e-12/bp?
19:29 < juul> i'm not on my laptop. is that a production system left accidentally open?
19:29 < kanzure> nah just a staging/development server
19:29 < juul> left accidentally open? or on purpose?
19:30 < kanzure> dunno
19:30 < juul> hm
19:32 < kanzure> juul, see pm for unrelated topic
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20:41 < kanzure> .title https://www.youtube.com/watch?v=o9n0tfutOp4
20:41 < yoleaux> OpenDrop V2 with Top Cover Slip - YouTube
20:43 < kanzure> https://www.youtube.com/watch?v=jpbUvSyeRg0&index=16&list=PL5AFDE0D7CCE51ACE
20:47 < kanzure> .wik indium tin oxide
20:47 < yoleaux> "Indium tin oxide (ITO) is a ternary composition of indium, tin and oxygen in varying proportions. Depending on the oxygen content, it can either be described as a ceramic or alloy. Indium tin oxide is typically encountered as an oxygen-saturated composition with a formulation of 74% In, 18% O2, and 8% Sn by weight." — https://en.wikipedia.org/wiki/Indium_tin_oxide
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20:59 < kanzure> polymerase stuff http://diyhpl.us/~bryan/papers2/polymerase/Molecular%20events%20during%20translocation%20and%20proofreading%20extracted%20from%20200%20static%20structures%20of%20DNA%20polymerase%20-%202016.pdf
21:04 < kanzure> nmz787: juul would like to make a spectrophotometer
21:04 < kanzure> ah nevermind. you spoke.
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21:34 < nmz787> did I tell juul to just buy one instead from http://www.science-surplus.com/products/spectrometers   ?
21:34 < nmz787> it doesn't do UV tho
21:41 < kanzure> .title https://www.youtube.com/watch?v=qUaFYzFFbBU
21:41 < yoleaux> Jurassic Park - Mr. DNA Sequence - YouTube
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22:11 < nmz787> juul: well dorsal-ventral patterning is a thing and it isn't "epigenetics" or new
22:12 < nmz787> huh, celery eh?
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23:29 < nmz787> huh, that jurassic park video shows a cesium chloride extract, I think
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--- Log closed Mon Jan 15 00:00:24 2018