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| chris_99 | https://hackaday.io/project/9205-blubeam-a-scanning-laser-microscope | 04:46 |
|---|---|---|
| yoleaux | 18 Jun 2016 06:11Z <nmz787> chris_99: 3d-printer with magnetometer to map magentics http://hackaday.com/2016/06/17/hackaday-prize-entry-visualizing-magnetic-fields/ | 04:46 |
| chris_99 | nmz787, saw that, thought it looked interesting! | 04:46 |
| chris_99 | anyone an idea what the resolution limits are with confocal microscopy | 04:54 |
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| JayDugger | Good morning, all you tag-eaten brains. | 06:21 |
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| streety | chris_99: https://en.wikipedia.org/wiki/Super-resolution_microscopy claims 250 nm | 07:21 |
| chris_99 | hmm, i thought it'd be better than that | 07:22 |
| streety | I get a voxel size (not the same as resolution) of 640 nm with a 10x objective | 07:22 |
| chris_99 | wait isn't that number normal microscopy | 07:22 |
| chris_99 | actually | 07:22 |
| chris_99 | yeah i'm pretty sure that's not confocal | 07:23 |
| streety | yeah, just reread and you're right | 07:23 |
| chris_99 | so itll definitely be below that number, but i'm not sure how much lower | 07:23 |
| streety | https://en.wikipedia.org/wiki/Super-resolution_microscopy#4Pi getting closer | 07:24 |
| chris_99 | i assume it depends somewhat on the pinhole size | 07:24 |
| streety | 100-150 nm? | 07:25 |
| chris_99 | hmm, i thought it'd be better than that actually | 07:25 |
| chris_99 | http://www3.mpibpc.mpg.de/groups/hell/publications/pdf/Appl._Phys._Lett._69_3644-3646.pdf mentions 50-100nm in the title, i'll keep looking | 07:27 |
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| kanzure | juul: drew seems to be anti hgp-write | 10:28 |
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| nmz787 | kanzure: does he want [other-organism]-write instead? ethics/moral issues??? | 10:33 |
| kanzure | dunno, i assume juul will be able to represent his views accurately, though | 10:33 |
| nmz787 | ah | 10:34 |
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| chris_99 | nmz787, did you see the confocal HaD link? seems intriguing | 10:53 |
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| kanzure | yashgaroth: have you read recent backlog? | 11:56 |
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| yashgaroth | regarding brain viruses? | 11:57 |
| kanzure | yashgaroth: i had a long phone call with human genome project 2 the other day | 11:58 |
| kanzure | yashgaroth: we can set lots of directional details | 11:58 |
| yashgaroth | for mass dna synthesis? | 11:59 |
| kanzure | they want to focus on external control of enzymes and polymerase if possible | 11:59 |
| kanzure | yes | 11:59 |
| kanzure | they are okay with doing inkjet dna synthesis stuff, but george church and others admit that their bottleneck is assembly | 11:59 |
| yashgaroth | could get a smidge of the money and try out the nicking + polymerase octamer system | 12:00 |
| kanzure | think bigger plz | 12:00 |
| kanzure | but yes we should do that | 12:00 |
| kanzure | actually we could probably do that without them anyway | 12:01 |
| yashgaroth | always nice to use their money, but yeah...by assembly do they mean the whole 3-billion genome, or smaller subunits? | 12:01 |
| kanzure | well their goal is human genome | 12:02 |
| kanzure | but yeah... "large strands of dna" in general. | 12:02 |
| kanzure | hybridization works so much better when you have 200 bp tails to match against, anyway | 12:02 |
| yashgaroth | well it's not like we need to stick to the normal number of chromosomes | 12:02 |
| yashgaroth | depends how human they want to keep the resulting organism | 12:03 |
| kanzure | they are open to whatever on that front, so yes we can do unusual numbers of chromosome if necessary | 12:04 |
| kanzure | since they are at an early stage, now is a good time for us to think about and then propose anything that might strongly influence long-term direction of their project | 12:05 |
| yashgaroth | well there's a lot to consider, making a human copy vs trying to improve on it, keeping it modular | 12:06 |
| kanzure | they are willing to fund expermental and theoretical things, even speculative stuff like all the weirdo polymerase ideas we have had (in fact, the project originator has spent a lot of time in the past brainstorming with me about electronically controlled polymerases) | 12:06 |
| kanzure | well the goal is synthesize long strands of dna | 12:07 |
| kanzure | or, assemble them in a way that does not take forever or that is not too frustrating | 12:07 |
| kanzure | there are some human aspects to this which can be added, but the core technology around synthesis is their primary mission. they are willing to entertain ideas about synthetic human genome engineering stuff like taking out chunks of dna or inserting high-efficiency replacements for certain areas of metabolism, although again their core mission is synthesis. | 12:07 |
| kanzure | http://diyhpl.us/~bryan/papers2/bio/The%20human%20genome%20project%20-%20write,%20hgp-write%20-%202016.pdf | 12:08 |
| yashgaroth | well, the more junk they're willing to cut out, the easier it'll be, hell ALU repeats are like 10% of the genome already | 12:09 |
| kanzure | imho they should use dna synthesis for making billions of inter-connecting proteins for the purpose of molecular nanotechnology (molecular lego), at which point a bunch of other fun projects become more easily possible | 12:09 |
| kanzure | they have good reason to want to synthesize even longer stuff; no use in making a single genome when you can make a million genomes, that sort of thing... | 12:10 |
| yashgaroth | true, cheap large synthesis is the main benefit | 12:11 |
| yashgaroth | how much of it are they willing to just clone out of the human genome? | 12:12 |
| kanzure | i think amost none of it. they want to do this like the synthetic yeast genome from last year. | 12:13 |
| yashgaroth | I can respect the principle but man a lot of that stuff you can get with two primers and polymerase | 12:14 |
| kanzure | i haven't checked but does this mean they determined that the yeast genome does not require any methylation to work as a functional yeast genome when inserted into otherwise un-nucleated yeast cells? | 12:15 |
| yashgaroth | not sure how much yeast care about methylation as a unicellular organism, though I suppose methylation would be easy enough to incorporate in the pamidites | 12:16 |
| kanzure | yes it's unclear to me that sstraight up dna synthesis is useful for genomes | 12:17 |
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| yashgaroth | you know if they're gonna try mice etc first, or is it straight to human? | 12:25 |
| fenn | the big bold taste of synthetic human meat | 12:25 |
| kanzure | yashgaroth: i expect that they will have many grants involved some that will be non-human... i don't know. | 12:26 |
| kanzure | we should probably figure out a few things they should be doing with all that $250M | 12:27 |
| kanzure | for example, metabolism optimization would be a good thing for them to try to do | 12:27 |
| kanzure | sperm with better flagella | 12:28 |
| kanzure | cell pores for dna uptake | 12:29 |
| fenn | it seems like a technology project more than a biology project | 12:29 |
| kanzure | obviously some basic disease stuff.. | 12:29 |
| fenn | unless someone figures out some magic with molecular machines | 12:29 |
| yashgaroth | well there's a million things to tweak, hell even if you just made the organism able to take up and propagate a megavirus that carried any potential upgrades | 12:29 |
| kanzure | well in the original human genome project there was a specific sequencing goal but also a bunch of grants for all sorts of somewhat related projects | 12:29 |
| kanzure | re: megavirus, yea that seems difficult because you can't really guarantee that all cells are equally accessible. i guess you could because otherwise how would the cells be feeding? hrm... | 12:30 |
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| yashgaroth | there's some accessibility concerns, but if it transfers cell-to-cell and has a regulatory switch to prevent reinfection, should be doable | 12:31 |
| yashgaroth | then you pop it into the blood and the brain, wait however long for it to spread, and bam you've got v1.1 | 12:32 |
| yashgaroth | it's bad enough us regulars are gonna get left behind, I don't want v1.0s to be like "aww man I was born a year too early for the hypersleep compatibility mod" | 12:33 |
| * kanzure marks down yashgaroth for "fear of missing out" | 12:34 | |
| yashgaroth | won't somebody please think of the ultrachildren | 12:34 |
| kanzure | in the long run, i would like to replace chunks of human biology with something more deterministic, even if it has to be specified by dna | 12:35 |
| yashgaroth | deterministic like how | 12:35 |
| kanzure | mechanical clockwork would be nice | 12:35 |
| kanzure | we could have a mechanical organelle attached to the cytoskeleton, and slowly transfer more functionality from the usual environment inside of the cell into the mechanical organelle's control and function | 12:37 |
| yashgaroth | I'm the first to admit biology sucks compared to a lot of electromechanical stuff, even at its possible best | 12:38 |
| kanzure | i don't think that chasing aging-related biology problems is going to be productive long-term, or other healthcare issues, because biology sucks and it breaks and is poorly designed, and i'm pretty sure we can make better designs for many of its components | 12:38 |
| fenn | biology is optimized for evolution | 12:39 |
| fenn | if things change your fancy rationally designed humans will maybe not adapt as well as baselines | 12:40 |
| kanzure | bah, whatever. if that was true, it would have more sandboxes where it tests protein function and then copies good protein function across all cells in the body. instead we have to wait a few hundred generations or something stupid like that. | 12:40 |
| kanzure | yeah i am sure that rational-design humans will have many problems, but they will be different problems with different tradeoffs | 12:40 |
| yashgaroth | we stopped relying on evolution a long time ago, normal humans don't adapt that well anyway, except maybe over hundreds of generations | 12:41 |
| fenn | well i can easily see designers throwing out a lot of starvation-mode adaptations in the name of performance | 12:41 |
| kanzure | yes that's a common pattern during refactors: oh just throw everything out, what do we need it for | 12:41 |
| yashgaroth | if they end up starving to death I don't think we'll have done a very good job with the rest of civilization | 12:41 |
| yashgaroth | which admittedly is a valid concern | 12:42 |
| fenn | anyway sign me up for hypersleep 2.0 | 12:42 |
| fenn | i don't know what it is but it sounds awesome | 12:42 |
| yashgaroth | but yeah most of the phase 1 mods via IVF is like "well they can run 10x farther than the best athletes but they do consume 20 thousand calories a day, oh well" | 12:43 |
| yashgaroth | nor do I fenn, that's why I'd like to keep their options open | 12:43 |
| fenn | a lot of this downloadable content stuff is a double edged sword | 12:43 |
| fenn | you can have an immune system linked to the internet to get antivirus updates daily, but then your immune system is linked to the internet... | 12:43 |
| kanzure | i would take the internet any day, rather than "linked to your colleagues at work and school" wtf | 12:44 |
| kanzure | i think that the rational human design stuff is going to be at first mostly for the sake of redundancy | 12:45 |
| kanzure | er, and of course should start with non-human anyway | 12:46 |
| fenn | speaking of which, why isn't that a thing? synthetic B-cells for specific antigens | 12:46 |
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| yashgaroth | well technically it is already for cancer immunotherapy | 12:46 |
| fenn | put it in a rabbit, inject all the school kids | 12:46 |
| fenn | thought cancer was T-cells | 12:47 |
| yashgaroth | ah true, well same principle applies, you gotta tailor the cells to be compatible with the host | 12:47 |
| yashgaroth | usually by pulling some out and modifying them, which costs an absurd amount | 12:48 |
| fenn | how many permutations are there? is it the kind of thing where you could have a dozen blood types and just keep them in stock? | 12:48 |
| kanzure | there's a few (recent?) things that convert blood types between each other | 12:48 |
| fenn | i mean MHC type | 12:49 |
| yashgaroth | several hundred, roughly | 12:49 |
| fenn | can you just include all of the types? | 12:50 |
| fenn | like this cell is type A AND type B AND type C ... type Z20 | 12:50 |
| yashgaroth | I suppose you could try heavily modding the cells to not present any antigens to the host, though that's tricky | 12:51 |
| fenn | eh i guess several hundred is not too bad | 12:53 |
| fenn | you only need a tiny speck of cell culture to inoculate an individual | 12:54 |
| yashgaroth | well, (several hundred)^3 if you consider all the HLA variants, but immunology is not my specialty | 12:56 |
| yashgaroth | making ghost cells that avoid the host immune system entirely might be more feasible, though viruses and cancer have been trying to perfect that for a long time | 12:57 |
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| nmz787 | IMO we have a lot of variation in human phenotype/genotype already... socioeconomic status, regional variation in climate and nutrient availability... seems like we have quite an array of adaptation ability in storage. Yes this might be overhead, but insurance always is. | 13:35 |
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| chris_99 | Can anyone think of a cheap mechanism to enable the rotation & positioning of a 35mm slide size diffraction grating & slit | 14:59 |
| fenn | yes | 15:23 |
| chris_99 | what were you thinking of fenn? | 15:26 |
| fenn | some sort of parallel kinematic planar actuator | 15:28 |
| fenn | flexures and electromagnets | 15:28 |
| fenn | but i dont know what you're doing so i didnt think further | 15:28 |
| chris_99 | i'm making a simple spectrometer with a slit and transmissive grating | 15:29 |
| fenn | why do you need to move anything? | 15:30 |
| chris_99 | i need to rotate the diffraction grating wrt the sensor | 15:30 |
| fenn | how much? 90 degrees? 1 degree? | 15:31 |
| chris_99 | the angle of incidence of the grating is around 40 deg, i dunno how much i'd need to rotate when calibrating though | 15:33 |
| chris_99 | sorry im wrong its nearer 13 degrees | 15:34 |
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| nmz787 | chris_99: speaker and DAC + driver FET? | 15:55 |
| nmz787 | (i.e. voice coils) | 15:55 |
| nmz787 | or maybe a solenoid? | 15:55 |
| chris_99 | oh sorry i wasn't clear, i just mean to manually rotate the grating for calibration, along with positioning the slit, i'm thinking maybe even something like modular hose might work with croc clips on | 15:58 |
| nmz787 | "Hypoglycemic benefit of cinnamon, tea, witch hazel, cloves, bay leaf and allspice lost by treatment with polyvinylpyrrolidone." | 15:59 |
| nmz787 | .title http://www.ncbi.nlm.nih.gov/pubmed?orig_db=pubmed&term=10725162 | 16:00 |
| yoleaux | Insulin-like biological activity of culinary and medicinal plant aqueous extracts in vitro. - PubMed - NCBI | 16:00 |
| chris_99 | http://www.tapwithus.com/ -- i'm wondering how hard that would be to learn to use | 16:02 |
| nmz787 | "The glucose oxidation enhancing bioactivity was lost from cinnamon, tea, witch hazel, cloves, bay leaf and allspice by poly(vinylpyrrolidone) (PVP) treatment, indicating that the active phytochemicals are likely to be phenolic in nature. The activity of sage, mushrooms, and brewers's yeast was not removed by PVP." | 16:03 |
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| kanzure | .wik microwriter | 16:57 |
| yoleaux | "The Microwriter is a hand-held portable word-processor with a chording keyboard. First demonstrated in 1978, it was invented by UK-based, US-born film director Cy Endfield and his partner Chris Rainey and was marketed in the early 1980s by Microwriter Ltd, of Mitcham, Surrey, UK." — https://en.wikipedia.org/wiki/Microwriter | 16:57 |
| kanzure | odd shape for a wearable, needs more accelerometers on a glove or something https://gest.co/technology | 17:00 |
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| kanzure | https://medschool.duke.edu/sites/medschool.duke.edu/files/pictures/Mouse_Connectivity.jpg | 18:07 |
| kanzure | http://www.neuroscience.cam.ac.uk/uploadedFiles/mcl45_php7hgneA.jpg | 18:07 |
| kanzure | http://neuroinformatics2011.org/abstracts/identification-and-classification-of-functional-modules-in-the-brain/image_default | 18:08 |
| kanzure | https://team.inria.fr/parietal/files/2012/08/connectivity_2014.png | 18:09 |
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| kanzure | "Individual differences in verbal creative thinking are reflected in the precuneus" https://www.researchgate.net/profile/Qunlin_Chen/publication/279737018_Individual_differences_in_verbal_creative_thinking_are_reflected_in_the_precuneus/links/55a128ee08aea54aa8143e95.pdf | 18:20 |
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| kanzure | "Reduced frontal cortex thickness and cortical volume associated with pathological narcissism" http://www.sciencedirect.com/science/article/pii/S0306452216300902 | 18:22 |
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| kanzure | ".. the Pathological Narcissism Inventory score, adjusting for age, sex, and total intracranial volume, was significantly negatively associated with cortical thickness and cortical volume in the right dorsolateral prefrontal cortex" | 18:23 |
| kanzure | "the score showed significant negative associations with cortical volume in the right postcentral gyrus, left medial prefrontal cortex (MPFC), and the cortical thickness in the right inferior frontal cortex (IFG)" | 18:24 |
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| kanzure | "Increased size of posterior ventral cingulate cortex is related to the working memory performance decline.[3]" | 18:30 |
| kanzure | "Thus, we have started developing a database of anatomical connections and architectonic features of the ferret brain, the Ferret(connect)ome, www.Ferretome.org. The Ferretome database has adapted essential features of the CoCoMac methodology and legacy, such as the CoCoMac data model" | 18:32 |
| kanzure | what an awful name | 18:32 |
| kanzure | *ferretome? | 18:32 |
| kanzure | ferrtome? | 18:32 |
| kanzure | "Vertebrate brains and evolutionary connectomics: on the origins of the mammalian 'neocortex'" https://www.researchgate.net/profile/Harvey_Karten/publication/283648861_Vertebrate_brains_and_evolutionary_connectomics_On_the_origins_of_the_mammalian_'neocortex'/links/566fb1ac08aec0bb67bf17ad.pdf | 18:37 |
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| kanzure | that is a good paper. | 18:59 |
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| not_unoriginal | anyone here know about exosphe.re | 21:54 |
| yashgaroth | sort of | 21:56 |
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| --- Log closed Mon Jun 20 00:00:34 2016 | ||
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