--- Log opened Mon Jul 31 00:00:36 2017
00:13 < mrdata_> i'm just not sure how you cause those to line up; seems to make assumptions about memory mapping
00:19 < Jenda`> there are also slides https://github.com/xoreaxeaxeax/sandsifter/blob/master/references/domas_breaking_the_x86_isa.pdf
00:20 < Jenda`> they seem to be shorter and more understandable than the paper
00:20 < fltrz> Jenda`: thanks for pointing it out, I just checked them and you're right
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03:45 < archels_> foreverlabs.com. interesting
03:46 < archels_> $7k total cost for extraction and lifetime storage of your own stem cells
03:46 < archels_> alternatively, $2.5k for the extraction and then $250 annually
03:46 < archels_> I'm surprised at how cheap they are offering this
03:52 < kanzure> gwillen: https://www.reddit.com/r/Bitcoin/comments/63f8le/you_can_now_bank_your_young_adult_stem_cells_and/
04:10 < archels_> haha
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04:48 < fltrz> how much does "full" sequencing an individual's human genome cost today?
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06:02 < kanzure> fltrz: $1k. see https://www.veritasgenetics.com/ for 30x coverage.
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06:35 < fltrz> kanzure: how does it compare to this MinION nanopore thing? they claim to sell a starter pack for $1k
06:38 < kanzure> veritas is more consumer-friendly; i'd prefer to have lots of nanopore sequencers though, yeah.
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07:13 < altersid_> fltrz: you'd likely need a lab around for nanopore seq, the coverage won't be high with lots of mistakes
07:14 < altersid_> (if 1k is what you would spend)
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08:09 < fltrz> I see, I am reading up on nanopore sequencing (wikipedia) in the semiconductor pore section, the current is in the plane of the pore, I but when I was reading the biological pores before I thought the current was from one halfplane to the other i.e. along the pore
08:12 < fltrz> and I was under the impression that the effect was the same as in https://en.wikipedia.org/wiki/Scanning_ion-conductance_microscopy#Working_principle
08:13 < fltrz> but instead of the escape surface between pippette and nonconducting target, the escape surface is the tiny pore size minus the base in the ssDNA
08:14 < altersid_> well, there are multiple ways of implementing nanoseq
08:15 < altersid_> in the implementation from oxford nanopore tech, the current is created by the flow of ions located in the buffer, passing through the nanopore protein
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08:16 < aeiousomething> hello
08:29 < JayDugger> Good monring.
08:33 < kanzure> "escape surface"?
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09:13 < fltrz> kanzure: imagine the pippette wall thickness to be infinitesimally thin, and that the pippette is orthogonal to and very close to a plane, then it would be the area of the cylindrical strip just beneath the end of the pippette
09:14 < fltrz> (the resistance of a conductor is hardly affected by its widest parts (with large cross-section area) but is mostly defined by the parts with the smallest cross-section)
09:17 < fltrz> for a fixed applied potential difference any current from the pippette to a reference electrode in the bath must pass through this thin cylindrical strip, so this resistance causes a decrease in current compared to the pippette being farther from the plane
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09:18 < fltrz> I was thinking the nano pore sequencing uses the same effect, but I remain in doubt because of the semiconductor pore section
09:20 < fltrz> the semiconductor pore section implies a kind of tunneling current where the current is not through the hole, but across with multiple electrodes arranged circularly around the pore
09:23 < fltrz> altersid_: is the current in the oxford nanopore tech the result of an applied potential difference? or somehow due to ssDNA passing?
09:24 < fltrz> what causes the device to be a consumable?
09:31 < kanzure> is this a question about device lifetime, or a question about my comment regarding consumer-friendly?
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09:36 < FourFire> archels_, awesome, I was considering investigating potential custom deals with fertility clinics for adult stem cell storage
09:42 < fltrz> I'm trying to understand the prices for sequencing
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09:57 < ybit> "Quantum tunneling takes time, new study shows: A new measurement disfavors the idea that electrons can escape atoms instantaneously." https://www.sciencenews.org/article/quantum-tunneling-takes-time-new-study-shows
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10:17 < gwillen> 03:52:57 < kanzure> gwillen: https://www.reddit.com/r/Bitcoin/comments/63f8le/you_can_now_bank_your_young_adult_stem_cells_and/
10:17 < gwillen> that, uh, doesn't seem to answer any questions, although maybe it raises some new ones :-P
10:35 < thundara_> gwillen: Questions about forever labs itself?
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10:35 < gwillen> just curious to hear various perspectives on it
10:35 < thundara> gwillen: The founders are pretty active on another message board
10:36 < thundara> https://hubski.com/pub/379661
10:36 < gwillen> yeah I've heard their perspective, I'm curious if people here think what they're trying to do is actually a good idea
10:36 < thundara> Ah
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10:38 < thundara> I imagine that depends on what disease you're worried about and how realistic the stem cell therapies there are :P
10:38 < nmz787> sup
10:41 < fltrz> I don't know much but I think: stem cells roughly form a 'genealogical tree' with fertilized egg at root and then different cell types at each node, the 'relatively higher' ones being called stem cells
10:43 < fltrz> so if bonemarrow is used the advantage is that the ones below could theoretically be easier to derive from them, but not the ones in other branches or higher up the genealogical cell lineage tree
10:44  * gwillen nods
10:45 < fltrz> on the other hand, the difference between the cell types (assuming no change in DNA as in for example immune system white blood cells!) is not a difference in DNA but in concentrations of cell (and vacuole) concentrations of chemical species
10:45 < gwillen> well, and epigenetic changes potentially
10:46 < gwillen> unless that was what you meant by 'change in DNA'
10:46 < fltrz> in a sense a cell type is a relatively stable point or limit cycle of the 'gene regulatory network'
10:46 < gwillen> ahhh, huh. That's interesting.
10:47 < fltrz> I never liked the term epigenetic, because I have always had the impression it referred to very specific mechanisms
10:47 < gwillen> mmm, *nod*
10:47 < gwillen> usually I think of methylation
10:47 < fltrz> yes most people refer to methylation when they mention epigenetic
10:49 < gwillen> anyway I also wonder about like, what's the chance the company would survive until one actually wanted the cells
10:49 < fltrz> I think of it more like a flip flop, the flip flop on a silicon die (i.e. the doping profiles and the connecting nodes etc) is like DNA, but it does not fully specify the state
10:49 < gwillen> and if they don't will the cells die with them
10:49 < gwillen> (they claim no, of course)
10:49  * gwillen nods
10:49 < fltrz> the flipflop is bistable, it can be in 0 state or in 1 state, but it can be pushed to the other state
10:50 < gwillen> yeah the comment about stable points of gene regulatory networks is very interesting
10:50 < fltrz> gwillen: good point
10:50 < gwillen> I had never read about those before
10:50 < gwillen> but that makes it sound like the cell has sort of a cell-type DFA
10:50 < gwillen> and you can push it between states with signalling molecules
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10:50 < gwillen> presumably most easily in the "more specific" direction, but not exclusively
10:51 < fltrz> it doesnt have to be deterministic, but it would be the easiest way to introduce the concept
10:51 < gwillen> the other thing I wonder is -- they sell this procedure as a super cool biotech fountain of youth, but if so, why isn't everybody in this channel already signed up and yelling about how great it is
10:52 < gwillen> (cost maybe, or availability, I suppose)
10:53 < fltrz> gwillen: I don't know, I didn't look them up yet, I have other priorities in life :)
10:53  * gwillen nods! 
10:57 < fltrz> anyway, the reason I am quite pessimistic is because I actually believe the annoying answer (cell types are 'stable points' of the chemical reactions in the cell/nucleus and or other vacuoles) is correct, yet implies that to objectively identify all cell types we need the reaction speed coefficients for each reaction
10:58 < fltrz> if we have the reaction rate coefficients, we can actually calculate the stable points for a specific individuals genome
11:00 < fltrz> once we have the cell types we can start investigating the behaviour of each cell type to find potential cancerous behaviour (assuming 'natural' cancer)... but radiation induced cancer... you need to sample the cancerous tissue and redo the calculations...
11:00 < fltrz> I tried to look at ab initio reaction rate computation... seems like we are very far from it...
11:03 < fltrz> I honestly believe uploading the mind will become feasible before *perfect DNA* therapy or instacure-cancer-as-if-it-was-a-cold will become feasible
11:04 < fltrz> and crazy AI will become feasible before uploading our minds
11:06 < kanzure> <-- just got done with human genome project infrastructure/technology working group conference call 2.
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11:11 < gwillen> kanzure: whoa, cool.
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11:20 < fltrz> gwillen: forgot to mention something else, again on the topic of reaction rates, the binary mechanism of genes is widely understood: a DNA sequence is transcribed->...->translated to protein or it isn't for some reason (transcription was blocked or whatever)
11:21 < fltrz> in programming binary bits are certainly usefull, but more usefull are numeric quantities that can take on more values, like integers, floats
11:23 < fltrz> so we observe different say lengths in people, not just 2 kinds: big guys and small guys. I think the differences for the similar protein between different individuals is not in functional binding
11:24 < fltrz> but I think the difference in similar proteins is predominantly variations in mass, which affects reaction rates, which affect the exact position of the stable fixed point
11:26 < fltrz> so say same skin cell type across individuals expressing more or less melanin (I assume its produced in skin cells, but I could be wrong, its just a didactic example) would have practically the same proteins in the production pathway
11:27 < fltrz> they would have pretty much identical functional chemistry, but across individuals masses would vary causing difference in reaction rates hence different equilibrium points for each individual
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11:30 < fltrz> those genes that can be easily varied by adding a couple amino acids to the protein, without being brittle by losing functionality because of the addition have an advantage in natural selection
11:31 < fltrz> varying mass of non-brittle proteins is much safer, than a bet on all-or-nothing change on a protein
11:37 < gwillen> hmmmm that's really interesting
11:42 < kanzure> gwillen: see http://diyhpl.us/wiki/transcripts/hgp-write/2016-05-10/ and http://diyhpl.us/wiki/transcripts/hgp-write/2017-05-09/
11:42 < kanzure> in particular http://diyhpl.us/wiki/transcripts/hgp-write/2016-05-10/ultra-safe-cell-line/
11:43 < kanzure> fltrz: i think you might like this one https://groups.google.com/d/msg/enzymaticsynthesis/WvDidIldm7c/q7aQTnmkAAAJ
11:44 < kanzure> it's a proposal for how to implement large-scale genome synthesis using crispr-cas9 (and other techniques) to iteratively edit an error correction codedd dna molecule.
11:44 < gwillen> huuuuh. Interesting.
11:44 < fltrz> thanks kanzure! that is interesting
11:45 < fltrz> on why masses affect reaction rates, see for example collision theory: https://en.wikipedia.org/wiki/Collision_theory
11:46 < altersid_> fltrz: yes, the current is a result of the flow of ions travelling through the pore due to a potential difference
11:46 < altersid_> this flow is quite constant when the pore is not obstructed
11:47 < altersid_> when a nucleic acid passes through it disrupts the current in a way which can be used to basecall the sequence
11:47 < altersid_> (ssDNA, or RNA)
11:47 < fltrz> altersid_: thanks, that confirms my suspicion that its the same effect as in scanning-ion-conductance-microscopy
11:48 < fltrz> but then I dont understand why the hardware would be consumable (apart from special rinsing or whatever) in the case of non-biological pores
11:49 < kanzure> iirc these pore do have a lifetime and they do get damaged
11:49 < fltrz> altersid_: and I also don't understand how the dna is made to slowly pass the pore
11:49 < altersid_> you can reuse a flowcell and wash it, but the number of available pore does decrease rapidly
11:51 < altersid_> during the library prep, you add a stalled motor enzyme on the 5' end of the molecule, this enzyme will become active once it connects with the nanopore protein and will process the molecule through the pore at a constant speed
11:51 < fltrz> are we sure the manufacturer isn't just doing "ink-cartride empty, computer-says-no" to buy new consumables? to fund research for next generation...
11:51 < altersid_> if you don't have it, the molecule will flush very rapidly through the pore and the signal will not be interpretable
11:52 < fltrz> altersid_: thanks for explaining the steady pull through the pore
11:53 < altersid_> np
11:54 < altersid_> they are still getting better at manufacturing the flowcells.. I don't think they are purposefully under optimising the pores so that they will degrade
11:54 < altersid_> but I am not employed by ONT :)
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11:57 < archels_> FourFire: how would you deal with the extraction procedure? I've not really much idea what's involved with that
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12:19 < kanzure> "Complex cellular logic computation using ribocomputing devices" http://www.nature.com/nature/journal/vaop/ncurrent/full/nature23271.html
12:19 < kanzure> cc ybit
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13:08 < ybit> thanks!
13:19 < docl> this was shared on facebook recently https://drive.google.com/open?id=0B9uXJVOTx_1qbFdXRDdWYi1JYUU (more orbital ring speculation)
13:20 < kanzure> .title
13:20 < yoleaux> Low Cost Design of an Orbital Ring.pdf - Google Drive
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13:21  * kanzure yoinks
13:21 < kanzure> http://diyhpl.us/~bryan/papers2/space/Low%20cost%20design%20of%20an%20orbital%20ring%20-%202017.pdf
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16:44 < kanzure> "Concurrency and privacy with payment channel networks" https://www.cs.purdue.edu/homes/pmorenos/public/paychannels.pdf
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17:20 < FourFire> archels_, you can probably figure that out with a good GP, at worst a bone marrow transplant specialist
17:21 < FourFire> but you need somewhere to store them first
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17:45 < kanzure> "The functioning of a cortex without layers" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5506093/ https://twitter.com/TC_papers/status/891109039714705408
17:46 < kanzure> "A major hallmark of cortical organization is the existence of a variable number of layers, i.e., sheets of neurons stacked on top of each other, in which neurons have certain commonalities. However, even for the neocortex, variable numbers of layers have been described and it is just a convention to distinguish six layers from each other. Whether cortical layers are a structural ...
17:46 < kanzure> ...epiphenomenon caused by developmental dynamics or represent a functionally important modularization of cortical computation is still unknown. "
17:46 < kanzure> "Here we present our insights from the reeler mutant mouse, a model for a developmental, “molecular lesion”-induced loss of cortical layering that could serve as ground truth of what an intact layering adds to the cortex in terms of functionality. We could demonstrate that the reeler neocortex shows no inversion of cortical layers but rather a severe disorganization that in the primary ...
17:46 < kanzure> ...somatosensory cortex leads to the complete loss of layers. Nevertheless, the somatosensory system is well organized. When exploring an enriched environment with specific sets of whiskers, activity-dependent gene expression takes place in the corresponding modules. Precise whisker stimuli lead to the functional activation of somatotopically organized barrel columns as visualized by intrinsic ...
17:46 < kanzure> ...signal optical imaging. Similar results were obtained in the reeler visual system. When analyzing pathways that could be responsible for preservation of tactile perception, lemniscal thalamic projections were found to be largely intact, despite the smearing of target neurons across the cortical mantle."
17:47 < kanzure> "However, with optogenetic experiments we found evidence for a mild dispersion of thalamic synapse targeting on layer IV-spiny stellate cells, together with a general weakening in thalamocortical input strength. This weakening of thalamic inputs was compensated by intracortical mechanisms involving increased recurrent excitation and/or reduced feedforward inhibition. In conclusion, a layer ...
17:47 < kanzure> ...loss so far only led to the detection of subtle defects in sensory processing by reeler mice. This argues in favor of a view in which cortical layers are not an essential component for basic perception and cognition. A view also supported by recent studies in birds, which can have remarkable cognitive capacities despite the lack of a neocortex with multiple cortical layers. In conclusion, we ...
17:47 < kanzure> ...suggest that future studies directed toward understanding cortical functions should rather focus on circuits specified by functional cell type composition than mere laminar location."
17:49 < kanzure> i bet this is superkuh's favorite twitterbot (it aggregates only thalamocortical neuroscience papers)
17:55 < kanzure> hm actually it seems to include a bunch of su8/pdms lithography stuff. seems to be a bug.
17:58 < kanzure> "Brain structural plasticity with spaceflight" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5460234/
17:59 < kanzure> "Spaceflight-induced neuroplasticity in humans as measured by MRI: what do we know so far?" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5445591/
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18:59 < ybit> aha, that was the paper queued to download
18:59 < ybit> this was a tab in the background https://wyss.harvard.edu/programming-cells-with-computer-like-logic/
19:04 < ybit> .title https://phys.org/news/2017-07-scientists-longstanding-biological-mystery-dna.html
19:04 < yoleaux> ybit: Sorry, that doesn't appear to be an HTML page.
19:04 < ybit> hah
19:04 < ybit> "Scientists solve longstanding biological mystery of DNA organization"
19:04 < ybit> i may have posted this previously
19:14 < fenn> what procedure is involved in extracting generic "stem cells" for future speculative purposes? is it like, a blood draw, or do they drill into your femur and stick a giant needle into your bone?
19:14 < fenn> or somewhere in between
19:16 < fenn> also why can't we use clones for this?
19:17 < fenn> some chinese researchers made human embryo clones right?
19:18 < fenn> and then there's all the pluripotent stem cell reprogramming stuff
19:18 < fenn> given these two technologies exist, i'm not sure stem cell banking makes sense anymore
19:19 < fenn> but maybe someone will ban cloning or reprogramming won't work reliably, who knows
19:22 < fenn> .title https://www.scientificamerican.com/article/stem-cells-made-from-cloned-human-embryos/
19:22 < yoleaux> Stem Cells Made from Cloned Human Embryos - Scientific American
19:24 < fenn> i expect most anti-aging research will be on these sorts of stem cells, rather thank banked stem cells, simply because most people haven't banked their stem cells
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19:25 < fenn> i wonder if you could get healthy eggs from a cloned embryo, to make more somatic cell nuclear transfer clones with
19:26 < fenn> without growing it past sesame seed size
19:28 < kanzure> "some chinese researchers made human embryo clones right?" was that the one where sooam technologies chief scientist was forcing his grad students to donate their eggs or something.
19:28 < fenn> no sooam is korean
19:29 < fenn> well anyway this one was in USA https://www.nature.com/news/human-stem-cells-created-by-cloning-1.12983
19:29 < fenn> heh electricity and caffeine, the sparks of life
19:30 < fenn> “People say, you did it in monkeys in 2007. Why did it take six years in humans?” Most of the time, he says, was spent navigating US regulations on embryo research.
19:30 < kanzure> you've surely seen page 3 by now of the iterated embryo selection paper http://www.nickbostrom.com/papers/embryo.pdf
19:31 < fenn> i read it a while ago but i don't remember
19:31 < kanzure> well it's not that interesting. embryo -> stem cells -> gametes, ova, sperm -> make more embryos. but they propose doing this in a context where dna synthesis would make more sense.
19:32 < kanzure> someone (in here?) was proposing a modification to this technique using... uh. bovine sperm?
19:32 < kanzure> "in vitro seminiferous tubule tech"
19:33 < kanzure> "so a thin slice of seminiferous tubules in a petri dish would be an interesting way to generate a very large amount of transformed sperm, as opposed to the current method of just waiting for a nice mutation, or doing IVF"
19:33 < fenn> i'm all for synthetic human genomes but it sounds like HGP-write is dragging its feet on that front
19:34 < kanzure> there was a meeting today; basically their current plan is to make roadmaps. they are currently kinda stuck figuring out if they want to directly coordinate 100 labs each producing chunks of dna, or if they want to focus on synthesis technology.
19:34 < fenn> bah
19:34 < JayDugger> humbug
19:35 < fenn> is venter involved in this? he at least seems to be interested in infrastructure development
19:35 < kanzure> in one of their recent documents (i think submitted to a funding agency) they mentioned something like "100k-1M bp", but i had to point out that the hgp-write 2016 timeline document actually calls for "100 million to 100 billion bp, at 1000x reduced cost, within 10 years".
19:35 < kanzure> afaik i have not seen venter around. this is mostly a show involving jef boeke and george church.
19:36 < kanzure> also they dropped the "h" from hgp-write but i think that was a stupid decision.
19:36 < fenn> super duper lame
19:36 < fenn> if not these people, who?
19:36 < kanzure> i would say that the biggest problem is that they haven't decided yet how to separate the "repeat Sc2.0 (synthetic yeast genome project)" proposals from the "let's encourage and fund synthesis technology development" proposals.
19:37 < kanzure> well these are so far mostly biologists... they are not engineers, they are not chemists.
19:37 < fenn> someone is going to be making human genomes and i'm sure everyone would rather it all be out in the open
19:37 < kanzure> hgp-write is not exactly an open initiative
19:37 < kanzure> literally they have the MPEG-LA crispr patent pool person managing their intellectual property working group
19:38 < kanzure> http://www.vocativ.com/428192/scientists-human-genome-struggle-transparency/
19:38 < fenn> how did everything go so wrong so quickly?
19:38 < kanzure> for biology culture this is already way outside their comfort zone
19:39 < fenn> oh come on, it's exactly the same stuff they had to do in order to finish the first HGP
19:39 < kanzure> the tech/infra working group is managed by jeff schloss, who worked for the first human genome project
19:39 < fenn> "100 lab collaboration" is dumb and wasteful
19:39 < kanzure> and he was telling a story today about how they really messed up by tying all of their funding to a chromosome-by-chromosome plan
19:40 < kanzure> and then it turned out that whole genome sequencing was a better idea, and they couldn't fund it because their money was already locked into the chromosome-by-chromosome plan.
19:40 < kanzure> sc2.0 was literally "each of 20-30 different labs is responsible for a separate yeast chromosome"
19:40 < kanzure> and many of the sc2.0 people are in hgp-write.
19:40 < fenn> why is this happening in new york instead of cambridge/boston?
19:41 < kanzure> hgp-write is mainly managed by nancy kelley and her engineeringbiologycenter.org in NY
19:43 < kanzure> "women are born with every egg they'll ever have, and it's a horrible process to get the eggs out, and they're expensive to manipulate and reimplant. but a super sperm factory, that'll dodge around all the issues with IVF."
19:44 < fenn> yeah so make the eggs in vitro
19:44 < kanzure> huh why did i say this: "there's a chemodrug that makes women regenerate eggs, btw" i have no idea what this is referring to.
19:44 < fenn> dunno
19:45 < kanzure> i am looking at a log of a chat i was having at like 3am, seems pretty random, and therefore i will conclude it is probably false. and/or i am too much stuck in bitcoin land.
19:46 < kanzure> fenn, one of my observations about hgp-write so far is that the whole group could be steamrolled by showing up with a better plan that is more technically accurate. they will adopt basically anything that looks reasonable at this stage. the trick though is that someone has to put the effort into writing down an idea.
19:46 < fenn> i remember reading about some platelet derived therapy for boosting egg fertility
19:46 < kanzure> i will gladly submit good ideas to the group and get things circulating, but unfortunately i don't have time to babysit proposals
19:47 < fenn> where is thomas jefferson when you need him
19:47 < kanzure> they are especially interested in roadmapping around synthesis technology development, large dna delivery into cells, large dna storage, testing, etc.
19:48 < kanzure> well i was thinking about sharing a link to http://diyhpl.us/~bryan/papers2/DNA/ but i have a tendency to be overwhelming and that might not be the ideal action at the moment.
19:48 < fenn> nobody reads papers :P
19:48 < fenn> did you forget
19:50 < kanzure> they have been communicating by copy-pasting a list of like 30 email addresses into each new email
19:51 < kanzure> i had to introduce them to doodle.com (for scheduling in large groups) so that they would sotp sending emails trying to negotiate mutually agreeable meeting times
19:51 < kanzure> and i had to tell them about the existence of mailing list software like mailman (as awful as it is..).
19:51 < kanzure> biology culture is all kinds of broken.
19:51 < JayDugger> Pun in there somewhere.
19:52  * fenn begins the arduous process of looking at a google docs file
19:53 < kanzure> "oh geeze here it comes i'm gonna have to use a browser that was compiled within the last 8 years."
19:53 < fenn> hey man i'm using the same computer but the software keeps getting slower
19:54 < fenn> i used to use chrome because it was fast
19:54 < kanzure> big problem with my transcripts is that i still can't seem to figure out how to type my own contributions. so almost everything i write is notably missing my own contributions.. but i'm like the best part of everything i do. so not capturing this makes life pretty miserable.
19:54 < fenn> now it's the slowest browser i have
19:54 < fenn> (and constantly steals my text input away from terminal)
19:56 < kanzure> i guess one parlor trick would be to switch to only speaking prepared statements, that way it's already pre-typed.
19:57 < fenn> is there some magic google docs url like "add /raw to the end of the url" to get it as plain text?
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19:59 < kanzure> sent you a thing.
20:12 < kanzure> yashgaroth: any thoughts about the meeting notes today
20:12 < yashgaroth> haven't looked yet, will do now
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20:30 < yashgaroth> $3.5 million for a "planning grant", imagine how many roadmaps we could write with that
20:31 < yashgaroth> I don't see the point of making a Y chromosome, even a modified one, when the money could be better spent on tech development
20:32 < kanzure> andrew's idea of outsourcing the roadmapping to the semiconductor industry is a good one. it would be nice if that happens.
20:33 < yashgaroth> can't be any worse at it than the current group
20:34 < kanzure> other thing i would like you to look at is the sperm production proposal that i was pasting a little while ago
20:34 < yashgaroth> uhhhh
20:34 < yashgaroth> oh the semeniferous tubule thing
20:34 < kanzure> "in vitro seminiferous tubule tech: so a thin slice of seminiferous tubules in a petri dish would be an interesting way to generate a very large amount of transformed sperm, as opposed to the current method of just waiting for a nice mutation, or doing IVF"
20:34 < kanzure> yes.
20:35 < yashgaroth> I had high hopes for sperm-mediated gene transfer but that sadly appears to have been bogus
20:35 < kanzure> i don't have context on this. elaborate?
20:36 < yashgaroth> some italian researchers claimed you could take a semen sample, spin it down and resuspend in PBS, and the sperm would take up foreign DNA with a decent efficiency
20:36 < yashgaroth> something about how the seminal fluid normally blocked the uptake
20:36 < yashgaroth> claimed to have done it in pigs, but people couldn't replicate it; would've been super easy since all you need is a centrifuge
20:37 < kanzure> huh. um. i could think of a number of ways of making it more likely to work.
20:38 < kanzure> sperm selection alone should be able to find you a good match for that...
20:38 < kanzure> also why pig, why not just study a bunch of random sperm in bulk, and figure out a species it works for?
20:38 < yashgaroth> I assume like cattle they're mostly impregnated by artificial insemination so the rest of the technology is easy, but not sure
20:39 < yashgaroth> well, not easy, but already extant, since they didn't do any IVF with it, just turkey baster
20:39 < kanzure> many different species of sperm are compatble with eggs (although some eggs are more universally compatible)-- sure, they might not be viable for more than a few hours, but it's enough to see some of the genetics at work.
20:39 < kanzure> *compatible
20:40 < yashgaroth> I don't think the italian government is big on chimeras, even at embryo stages. they are catholic after all
20:41 < kanzure> i'm still tickled by the existence of the "humster" hamster + human sperm test: https://en.wikipedia.org/wiki/Hamster_zona-free_ovum_test
20:41 < yashgaroth> I do think viral injection into the testes is a solid way forward, since they're immune privileged, and you can actually detect transformed sperm pretty easily
20:42 < kanzure> i'm not very familiar with the genetic environment inside sperm
20:42 < kanzure> lotta ribosomes?
20:42 < yashgaroth> extremely compacted DNA, very little protein
20:42 < yashgaroth> egg's got all the machinery
20:42 < kanzure> and what about across different species, do any of them have high protein content
20:43 < kanzure> gfp fluorescent sperm would be a good way to do selection on transformation result/efficiency
20:43 < yashgaroth> I doubt it, they're all selecting for speed...though non-mammals might, since there's a broader range of impregnation strategies
20:43 < yashgaroth> well exactly, you transform the progenitor cells so the mature sperm actually have a little GFP crammed in there
20:44 < yashgaroth> or a surface protein so you can just pull them down
20:44 < kanzure> chromatography filtering of cells by surface protein markers will work ? what?
20:45 < yashgaroth> not traditional packed-bed chromatography, but you could coat a membrane, maybe use magnetic beads
20:45 < yashgaroth> you don't need that many to survive
20:46 < yashgaroth> still, FACS is cheap enough once you have the machine, but it's an option
20:47 < fenn> what are you transforming with? a chromosome?
20:48 < fenn> hard to imagine a sperm picking up an entire chromosome without even a nudge
20:48 < yashgaroth> a big virus if you do injection, but if you can culture the tubules then the limit is much higher
20:48 < yashgaroth> the sperm-mediated gene transfer was just plasmids, single gene
20:48 < kanzure> well i was thinking rna interference but i don't know why
20:48 < fenn> do plasmids work in mammals?
20:49 < yashgaroth> sort of, I think they were linearized so they'd get integrated, but if you don't have to worry about immune rejection you could use episomal replication
20:50 < yashgaroth> or an integrase for that matter
20:52 < kanzure> eggs should be replaced with arbitrary virus-penetrable cells. and sperm should be replaced with viruses.
20:53 < yashgaroth> I know right
20:53 < fenn> i sort of enjoy not having babies falling out of my ears
20:53 < kanzure> what are you talking about, your ear sheds cells all the time.
20:54 < fenn> but they don't ask for child support payments
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20:55 < kanzure> there was a good defcon presentation this year from intel's chief medical officer talking about biosecurity and gene therapy, https://twitter.com/bcrypt/status/891739574669459456
20:55 < fenn> why does intel have "chief medical officer" as a position?
20:56 < kanzure> "exploits targeted by damage" https://pbs.twimg.com/media/DGAYZyMVwAEP12F.jpg:large
20:58 < kanzure> dunno, probably they have clinical studies that they are vaguely involved in, or they are interested in the healthcare industry in some capacity.
20:58 < kanzure> .. and somehow their chief medical officer is also someone who gives relevant talks at defcon, somehow.
21:07 < kanzure> bitcoin core visits japan: https://bc-2.jp/archive/season1/materials/0104_performace.pdf (japan has recently adopted bitcoin on a large scale for payments)
21:17 < kanzure> this is actually a really good presentation.
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