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02:24 < ebowden> What is mukbang?
02:25 < ebowden> Oh. Well, we have that too.
02:25 < ebowden> A fat, shirtless streamer who scarfs down food on camera whilst the twitch audience calls him "M'lord".
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05:56 < JayDugger> kanzure, fenn, nmz787, you have figures of merit for launch other than $/kg: launch availability (limited by both facility and launch window), range of orbits to which a payload can get delivered, payload capacity (dimensions and mass), and probably a batch of other things obvious to people who played more KSP than me.
05:57 < JayDugger> But no, Launch Loop looks too big to work.
06:05 < JayDugger> On the other hand, Lofstrom is smart, and continues to work on it. http://launchloop.com/RecentChanges
06:11 < kanzure> "A homing CRISPR mouse resource for barcoding and lineage tracing" https://www.biorxiv.org/content/early/2018/03/12/280289 https://twitter.com/biorxivpreprint/status/973166966264487936
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06:23 < kanzure> .title https://news.ycombinator.com/item?id=16591962
06:24 < yoleaux> Show HN: Where is Sci-Hub now? | Hacker News
06:24 < kanzure> https://whereisscihub.herokuapp.com/
06:24 < kanzure> https://whereisscihub.herokuapp.com/go
06:24 < kanzure> http://sci-hub.tech/
06:24 < kanzure> http://80.82.77.83/
06:24 < kanzure> http://80.82.77.84/
06:25 < kanzure> https://paperdownloader.cf/
06:26 < kanzure> https://www.wikidata.org/wiki/Q21980377
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06:32 < kanzure> .wik limesdr
06:32 < yoleaux> "This article provides a list of commercially available software-defined radio receivers." — https://en.wikipedia.org/wiki/List_of_software-defined_radios
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07:57 < fenn> JayDugger: my preferred "alternative" launch technology is jordin kare's laser thermal rocket up to suborbital 200km or so, where it's caught by a two stage rotating tether, inclination of your choice
07:58 < fenn> the laser part works even at very low vehicle mass and can be scaled directly from a test setup to continent-spanning
07:58 < fenn> all mass production, not finicky large composite layup
07:59 < fenn> tethers can change inclinations and eccentricities more or less arbitrarily
08:00 < fenn> also they bootstrap by lifting more tether material and solar panels
08:01 < fenn> launch loop scales poorly in comparison
08:06 < kanzure> typetypetype
08:10 < fenn> sci-hub is on the beach enjoying a pina colada
08:20 < kanzure> Baker van Deursen 2016, "Naturally occurring p16Ink4a-positive cells shorten healthy lifespan"?
08:20 < kanzure> minus the question mark
08:24 < kanzure> http://www.epigenetics.com.ua/
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08:34 < fenn> http://www.epigenetics.com.ua/wp-content/uploads/2016/02/spotted-flies-circle.001-1024x768.jpg flies of the world, it's time to set aside our differences, and come together. sing with me
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08:42 < kanzure> some papers on contributions to longevity by clearing p16Ink4a-positive cells http://diyhpl.us/~bryan/papers2/longevity/p16Ink4a-positive-cells/
08:43 < fenn> what is p16Ink4a?
08:43 < kanzure> "They have a chemical, AP20187 (AP), which activates a transgene, INK-ATTAC, which kills senescent cells. The paper title says "Naturally occurring p16Ink4a-positive cells shorten healthy lifespan", by which they mean that their transgene and AP extended lifespan 20%. Implementing this requires something like AAV therapy, which is why I didn't read it carefully, as I figured producing AAV is ...
08:43 < kanzure> ...beyond me."
08:44 < fenn> it's a tumor suppressor because it implements senescence directly?
08:48 < kanzure> p16 is a tumor suppressor. p16Ink4a is some variety of it which isn't explained well.
08:48 < kanzure> "p16Ink4a overexpression in cancer: a tumor suppressor gene associated with senescence and high-grade tumors" https://www.nature.com/articles/onc2010614
08:49 < fenn> "INK4a/ARF (Inhibitor of Kinase 4/Alternative Reading Frame) family, prevent the progression of the cell cycle. Because these genes are instrumental in prevention of tumor formation, they are known as tumor suppressors."
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08:49 < fenn> yeah it should just be p16
08:51 < fenn> god dammit i'm reading about cancer
08:51 < fenn> what the hell
08:51  * fenn does something useful
08:52 < kanzure> found this thru someone who was looking for siRNA things
08:52 < kanzure> i mean, siRNA transhumanist low hanging fruit things
08:54 < kanzure> INK-ATTAC is already on http://diyhpl.us/wiki/genetic-modifications/
08:54 < kanzure> heh!
09:05 < kanzure> "Muscle gene therapy" http://www.springer.com/us/book/9781441912053
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09:38 < maaku> justanotheruser: if you're using GROMACS it's fine for non-reactive domains
09:38 < maaku> non-reactive and not highly stressed configurations
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09:43 < maaku> It's been almost 10 years since I looked at NanoEngineer. My recollection is that it has a built-in molecular dynamics simulator for the CAD interface. I wouldn't trust the results of that, at all.
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09:44 < kanzure> depends on what you mean by built-in
09:45 < maaku> It has a GROMACS plugin, which should give reasonable results for stable, non-stressed molecules (which doesn't describe many things people have built with NE-1!)
09:45 < maaku> But, e.g., DNA-origami and such would be fine. As would simple buckyball and nanotube structures.
09:46 < maaku> But the "round" structures here wouldn't work : http://www.zyvex.com/nanotech/visuals.html
09:46 < maaku> Because they have internal stresses that you'd need ab initio simulations to prove out
09:48 < maaku> (GROMACS would be really bad at deciding whether these stresses result in broken bonds.)
09:48 < maaku> kanzure: the UI has a basic spring-based model for attaching atoms, right?
09:49 < kanzure> yes point-and-click atom connection stuff
09:54 < maaku> kanzure: you might be interested in this: http://idav.ucdavis.edu/~okreylos/ResDev/NanoTech/
09:54 < maaku> I played with it when I was at NASA. using VR interface to construct bucky shapes
09:55 < maaku> VR was incredibly useful at giving a sense of scale and a geometric intuition. NE-1 with this interface on an HTC Vive or something would be really slick
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09:57 < kanzure> ehh i'm not interested in that until after the initial commercial applications doc.  too much fun stuff that is too expensive to construct, otherwise.
09:58 < maaku> For sure. Just FYI I'm unlikely to be able to contribute to that anytime soon (next few months)
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11:41 < nmz787_> maaku: I tried this on my oculus rift http://autode.sk/rhodopsin
11:41 < nmz787_> maaku: also the google app, which was sort of a SketchUp for VR, was quite intuitive to use
11:42 < nmz787_> that's not so useful for molecular stuff, but maybe some molecular modelling app developers could steal cues
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14:05 < kanzure> dystrophin protein's gene is 2.4 megabases
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14:47 < kanzure> "Targeted plasmid integration into the human genome by an engineered zinc-finger recombinase" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3177191/
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14:49 < kanzure> https://www.sigmaaldrich.com/life-science/zinc-finger-nuclease-technology/compozr-kit.html
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15:32 < nmz787_> it would be cool if we found a version-control system embedded in DNA or genes
15:32 < nmz787_> like that 2.4 megabases, might actually just be full of old commit metadata or something
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16:19 < CaptHindsight> nah, bad release branches just die off  :)
16:22 < CaptHindsight> sigma aldrich with its 00 pricing, all regular material prices have 00 added on to the ends
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18:12 < kanzure> hyperblort
18:14 < CaptHindsight> http://science.sciencemag.org/content/359/6381/1283
18:15 < CaptHindsight> Mutation dynamics and fitness effects followed in single cells
18:15 < CaptHindsight> "1% of mutations were lethal; nonlethal mutations displayed a heavy-tailed distribution of fitness effects and were dominated by quasi-neutral mutations with an average cost of 0.3%."
18:16 < CaptHindsight> ~20,000 mutations genome-wide over hundreds of generations
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18:35 < kanzure> alright time for wacky biology crazy hour
18:35 < kanzure> why not make a suspension of mitochondria and do cellular fusion straight into the mitochondria?
18:36 < kanzure> human mitochondrial genome is tiny like 20-30 kb
18:36 < kanzure> then inject the mitochondria into other cells or whatever you want
18:36 < kanzure> you could also freeze the mitochondria or put them in macroporous beads and shoot them into cells with ballistics
18:38 < kanzure> cell fusion looks really suspicious and i'm not really sure how much it's taking from chromosome cross-over techniques, sexual reproduction, bacterial conjugation, or even sperm-egg fertilization stuff
18:38 < kanzure> but i keep hearing about yeast-mammalian cell fusions and stuff. and that's pretty wild.
18:39 < kanzure> .wik microcell-mediated chromosome transfer
18:39 < yoleaux> "Microcell Mediated Chromosome Transfer (or MMCT) is a technique used in cell biology and genetics to transfer a chromosome from a defined donor cell line into a recipient cell line. MMCT has been in use since the 1970s and has contributed to a multitude of discoveries including tumor, metastasis and telomerase suppressor genes as well as  …" — https://en.wikipedia.org/wiki/Microcell-mediated_chromosome_transfer
18:40 < kanzure> why hasn't this been used to transfer a neochromosome into a mesenchymal stem cell line and inject that into human bloodstream? what gives.
18:41 < kanzure> also, are there mitochondria-only "cell" cultures?
18:44 < kanzure> and can you do transfection on those mitochondria cultures and can you insert the mitochondria back into cells
18:45 < kanzure> plant protoplast fusion seems to work
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18:46 < kanzure> it's not clear to me why not use electroporation during the PEG-based cell conjugation techniques... or could be separate new technique. get the cells close enough together, zap 'em while their membranes are overlapping, and pray that the chromosomes and plasmids are actually transmitted correctly.
18:47 < kanzure> molecular biology friendo says mitochondrial transfection is real thing
18:47 < kanzure> and "rho mitochondria" have deleted mitochondrial DNA
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18:49 < kanzure> need new mitochondrial genome anyway
18:50 < kanzure> .wik cardarine
18:50 < yoleaux> "GW501516 (also known as GW-501,516, GW1516, GSK-516 and on the black market as Endurobol) is a PPARδ receptor agonist that was invented in a collaboration between Ligand Pharmaceuticals and GlaxoSmithKline in the 1990s, was entered into clinical development as a drug candidate for metabolic diseases and cardiovascular diseases, and was  …" — https://en.wikipedia.org/wiki/Cardarine
18:52 < kanzure> "my first interest would be in removing 5+ bp repeats from the genome, as they cause deletions"
18:55 < kanzure> "multi-virus resistance would remove the ability to do targeted insertions with viruses"
19:00 < kanzure> .title http://www.med.tottori-u.ac.jp/chromosome/
19:00 < yoleaux> 鳥取大学 染色体工学研究センター
19:00 < kanzure> http://www.med.tottori-u.ac.jp/chromosome/9520.html
19:01 < kanzure> aww wrong about rho mitochondria. just cells without mitochondria. fooey.
19:02 < kanzure> mitochondria-targeting bacteriophages tho, that might be useful
19:09 < kanzure> .wik cell fusion
19:09 < yoleaux> "Cell fusion is an important cellular process in which several uninuclear cells (cells with a single nucleus) combine to form a multinuclear cell, known as a syncytium. Cell fusion occurs during differentiation of muscle, bone and trophoblast cells, during embryogenesis, and during morphogenesis." — https://en.wikipedia.org/wiki/Cell_fusion
19:09 < kanzure> .wik cell-cell fusogens
19:09 < yoleaux> "Cell–cell fusogens are glycoproteins that facilitate the fusion of cell to cell membranes. Cell-cell fusion is critical for the merging of gamete genomes and development of organs in multicellular organisms. It drives cell membrane protrusions and fusogenic protein engagement." — https://en.wikipedia.org/wiki/Cell-cell_fusogens
19:12 < kanzure> "Sperm-egg fusion: events at the plasma membrane" http://jcs.biologists.org/content/117/26/6269
19:12 < kanzure> why not just inject a intracellular parasite and eject dna from that
19:14 < kanzure> mitochondrial bacteriophages seem to exist but it's really hard to find mitochondrial parasites because of all the "mitochondria was a parasite!!!" noise
19:16 < kanzure> .wik myzocytosis
19:16 < yoleaux> "Myzocytosis (from Greek: myzein, (μυζεῖν) meaning "to suck" and kytos (κύτος) meaning "container", hence referring to "cell") is a method of feeding found in some heterotrophic organisms." — https://en.wikipedia.org/wiki/Myzocytosis
19:16 < kanzure> " is also called "cellular vampirism" as the predatory cell pierces the cell wall and/or cell membrane of the prey cell with a feeding tube, the conoid, sucks out the cellular content and digests it.
19:16 < kanzure> "
19:22 < kanzure> "Vesicles in electric fields: Some novel aspects of membrane behavior" http://www.mpikg.mpg.de/th/people/dimova/publications/Dimova%20SoftMat%2009.pdf
19:25 < superkuh> Also interesting, purely lipid bilayers (not biological, synthetic, no proteins) and vesicles can show quanta of membrane current just like ion channels by forming transient pores.
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19:32 < kanzure> "Designer diatom episomes delivered by bacterial conjugation" https://www.nature.com/articles/ncomms7925
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19:32 < kanzure> "Direct transfer of whole genomes from bacteria to yeast" https://www.nature.com/articles/nmeth.2433
19:33 < kanzure> "Generation of transgenic mice with megabase-sized human yeast artificial chromosomes by yeast spheroplast–embryonic stem cell fusion" https://www.nature.com/articles/nprot.2013.093
19:40 < kanzure> "gene electrotransfer clinical trials" https://www.sciencedirect.com/science/article/pii/S0065266014000078 (electroporation)
19:42 < kanzure> nuclei injection for egg fertilization without sperm http://www.sciencemag.org/news/2001/07/egg-fertilized-without-sperm
19:48 < kanzure> "CNS-restricted transduction and CRISPR-Cas9-mediated gene deletion with an engineered AAV vector" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5330941/
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19:54 < kanzure> why not just focus on central nervous system gene therapy? ain't that immune privileged anyway?
20:04 < kanzure> "Enhancing the clinical potential of AAV vectors by capsid engineering to evade pre-existing immunity" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207363/
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20:40 < nmz787_> sup
20:41  * nmz787_ reads wacky bio hour backlog
20:42 < nmz787_> excuse me, wacky bio crazy hour
20:49 < kanzure> YOU ARE NOT EXCUSED
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21:30 < nmz787_> .wik electrofusion
21:30 < yoleaux> "Electrofusion is a method of joining MDPE, HDPE and other plastic pipes using special fittings that have built-in electric heating elements which are used to weld the joint together." — https://en.wikipedia.org/wiki/Electrofusion
21:30 < nmz787_> oh well, not that
21:30 < nmz787_> anyway, using an electroporator to fuse cells is definitely a thing
21:42 < nmz787_> is "face binding" a thing? akin to foot binding, like they did to keep feet small or whatever.
21:43 < nmz787_> oo
21:43 < nmz787_> .wik artificial cranial deformation
21:43 < yoleaux> "Artificial cranial deformation or modification, head flattening, or head binding is a form of body alteration in which the skull of a human being is deformed intentionally." — https://en.wikipedia.org/wiki/Artificial_cranial_deformation
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--- Log closed Fri Mar 16 00:00:20 2018