2015-10-09.log

--- Log opened Fri Oct 09 00:00:52 2015
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@nmz787is there some world map (google-something?) that shows you maps of the world through-time/history?00:05
@nmz787like with a slider bar for time00:06
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kanzure"patents were a dumb idea" https://news.ycombinator.com/item?id=10358640 yay05:29
kanzure"the milky way at different wavelengths" http://www.chromoscope.net/05:30
kanzurecommentary, https://news.ycombinator.com/item?id=1035866005:30
kanzure"quantum effects in large-scale systems" http://nautil.us/issue/29/scaling/how-big-can-schr246dingers-kittens-get05:32
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kanzuresomething about decapitating a mouse http://nautil.us/issue/29/scaling/why-the-russians-decapitated-major-tom05:34
kanzure"As planned, Major Tom’s organs were dissected and split among specialists from six countries, resulting in 70 studies. His brain was subdivided in smaller parts—frontal cortex, visual cortex, hypothalamus, hippocampus, striatum, and substantia nigra—some of which were sent to Vladimir Naumenko, a senior researcher from the Russian Institute of Cytology and Genetics. In a study published in July 2014, Naumenko concluded that ...05:34
kanzure... “spaceflight decreased the expression of crucial genes involved in dopamine synthesis.”"05:34
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archelsbut was it spaceflight per se?05:41
kanzure50-lane highway https://en.wikipedia.org/wiki/G4_Beijing%E2%80%93Hong_Kong%E2%80%93Macau_Expressway05:41
archelsthat's 50 toll booth lanes though, right05:42
kanzurehttp://i.huffpost.com/gen/3514284/thumbs/o-BEIJING-HONG-KONG-900.jpg?205:42
kanzurehm?05:42
archelsnot actually any long stretch of 50 lane highway05:43
kanzureoh :-/05:44
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archelspretty steampunk  http://i.imgur.com/8Jr66RL.jpg05:52
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kanzurearchels: what did you think of that blue brain project paper from yesterday?06:29
kanzurehave you looked06:29
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streetyis the lm317 the way to go for that nmz787? How much power does the laser need? My first thought would be a switched mode power supply would be the way to go06:45
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archelskanzure: "Reconstruction and Simulation of Neocortical Microcircuitry"?07:06
* archels looks07:06
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archelsoh, they didn't do a full-volume reconstruction07:19
archelsthey just rotated/perturbed a few stereotypes to fill the volume07:20
archelsthey also classify neurons somewhat rigidly into this "Petilla terminology", while it's pretty much accepted now that it's a continuum07:23
kanzureso they weren't doing their "statistically-informed generation of neural topology" technique?07:24
archelsit's a reasonable pragmatic choice at this point in time though, I wouldn't know how to sidestep that even for EM tech at present07:24
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kanzureEM?07:27
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archelsIn order to further increase morphological diversity, a cloning algorithm was implemented. This algorithm took07:29
archelseach morphology and injected noise into branch lengths and rotations, leaving the overall branching structure07:29
archelsunchanged, but resulting in completely unique space-filling for each clone.07:29
archelsand07:29
archelsAt each bifurcation point, there were two07:29
archelssubtrees, each of which were rotated by a degree sampled from a Gaussian distribution of mean 0° and07:29
archelsstandard deviation 10°.07:30
archelsthat's their cloning process... so just some statistical perturbations07:30
archelsEM as in, electron microscopy07:30
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archelsI guess electrophysiological classification under an EM sectioning process is out07:34
archelsnot sure how far they've come integrating RNA sequencing into that process07:35
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archels(the videos of the BBP paper are kinda pretty, so long as you're not put off by the lack of detail)07:37
archelsbut might be nice for highschool presentations07:38
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kanzuremodeldb mercurial repositories http://neuro.med.yale.edu/hg07:59
kanzurerecent random thing from that page, http://neuro.med.yale.edu/hg/181967/CutsuridisPoirazi2015/rev/4458d5a1a2c108:00
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kanzure"calcium accumulation into a volume of area*depth next to the membrane with a decay (time constant tau) to resting level given by the global calcium variable cai0_ca_ion"08:01
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kanzure"slow Ca-dependent potassium current"08:03
kanzure"cylindrical coordinate system  with constant annuli thickness to center of cell. Note however that the first annulus is half thickness so that the concentration is second order correct spatially at the membrane or exact edge of the cell."08:04
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gnushahttps://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=93922489 Bryan Bishop: short summary of dna synthesizer for maaku >> http://diyhpl.us/diyhpluswiki/dna/synthesis/notes/08:18
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gnushahttps://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=08:26
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gnushahttps://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=98445094 Bryan Bishop: better explanation of hplusroadmap >> http://diyhpl.us/diyhpluswiki/index/08:43
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kanzuremaaku: summary has been written, i'd be happy to extend the text to include whatever you identify as missing when you look http://diyhpl.us/wiki/dna/synthesis/notes/#summary08:50
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maakukanzure: hey thanks!10:19
kanzuremaaku: anything missing from it? plz spew generic questions10:20
maakukanzure: is the inkjet able to get accomplish precise manufacturing?10:22
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kanzuremaaku: inkjet printheads are amazing and you're missing out10:24
maakureading the summary sounds like you're doing spray-and-pray of A, C, T, and G10:24
kanzureeach droplet is a separate reaction chamber10:24
maakui see...10:24
kanzuresurface tension prevents the droplets from merging (and also the great distance between individual droplets)10:24
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maakuok so seach deposited droplet is a reaction chamber, that's something I was missing from the description10:25
kanzurewere you thinking "nanometer-precision deposition and stacking"?10:26
maakukanzure: yes, which is why I thought it was crazy10:26
maakuwhat's the two-sentence summary of how you get long strands of dna from that?10:26
kanzurereaction yield prevents superlong dna strands because even with 99.99% yield at each step you are going to get at least one error by the time you hit 100 bp length10:26
kanzuresooo instead you have to conjugate separate dna molecules from different reaction chambers. the mechanism of introducing them into physical proximity in a programmed, control way is still undecided.10:27
kanzures/conjugate/ligate (combine)10:27
maakuok so let's see if I understand: using traditional techniques you make a <100bp (<10bp?) dna strand, and using an inkjet you place droplets containing these and the necessary joining catalysts on a surface10:30
kanzurepopular proposals for this have included: use pipettes to move the samples around and conduct reactions; come up with single-pot reaction biochemistry with enzymes to ligate the dna molecules together; use lasers to push microbeads (from inside the droplet reaction chambers) around; use liquid crystal matrix displays and photoconduction to move droplets of water; etc.10:30
maakuthen as the droplets join the pieces join together?10:30
kanzuretraditional technique is giant column that you pump the reaction reagents through, dna strands are "grown" on the material packed into the column10:30
kanzureas the droplets join, there is a mixing of the reagents from the original reaction outputs, but then another reaction has to occur to get the molecules to join together10:31
maakuright, but you've positionally placed the necessary reagents and catalysts close together10:32
kanzurethe technique for synthesizing a strand of dna in a droplet is much more well understood than "what the heck are we going to do to conjugate the dna molecules together?" -- can't really have a pipetting robot that focuses on 1 micron diameter droplets. very hard to do.10:32
kanzureyes basically10:32
kanzure((and even if you do have a 1 micron droplet pipetting robot, you have 100 million droplets on the surface anyway, so certainly can't be some linear robot that pipettes each droplet individually; would take forever and never get done))10:33
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kanzureto be even more specific, there has been a previous inkjet dna synthesizer project where the team was able to print dna on a surface with i think it was 10,000 drops or whatever, but they were just leaving the dna there (for a technique called dna hybridization arrays). so they didn't even bother to try to conjugate the dna molecules together.10:34
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maakukanzure: at what point does the DNA start folding?10:38
maakuI assume that would be the upper limit on utility of this technique10:38
kanzuresome of the conjugation techniques (wait, all of them?) require enzymes and basically the reaction conditions for polymerase chain reaction, which involves cycles of heating and then cooling. the enzymes are good at grabbing on to the dna molecule and finding the ends.10:39
kanzureand the temperature also changes the behavior of the dna molecule10:39
kanzureand the enzymes10:39
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fenn"100s of millions of drops per second" is not correct10:44
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fennmaaku the inkjet only holds single bases, not strands10:47
fennthe strands are formed on the surface10:47
fennfor DNA origami, it only folds when you add the complementary sequence10:47
maakufenn: I'm thinking more regular old chromosome folding10:48
kanzurethe $5k printhead seemed to do ~200 million drops/sec10:48
fennwell, that's the goal. supposedly DNA origami is a bitch because the sequences like to fold spontaneously10:48
kanzuredna also twists and contorts into weird shapes, isn't just folding10:48
maaku"because the sequences like to fold spontaneously" <-- yeah that's my worry10:48
maakuit's just something you got to try and see though10:49
kanzureenzymes are good at handling long dna molecules10:49
kanzureif you created a dna molecule so long that it had physical twisting and other behavior that enzymes can't completely deal with yet, you could do directed evolution of enzymes to handle progressively longer dna molecules.10:50
kanzurebut there are species with superlong genomes and the enzymes for handling those genomes are mostly the same as any other10:50
fennyou expect way too much from evolution10:50
fennyou can't just dump a truck full of pigs from an airplane and expect to get a superpig10:50
kanzurenah that was based on informed expectations from known-mutations we've already seen10:50
kanzureright, you look at the damage to the pigs, find the least damaged pigs, and then breed those together10:50
maakukanzure: right. so I was asking because I'm trying to figure out how this is used to create a whole chromosome (e.g. 1G base pairs)10:51
maakuso you build up to large (1k? 1M?) segments, and then do more traditional biochemistry to stitch together the pieces10:51
kanzureonce you have superlong dna molecule, conversion into an actual chromosome is less problematic10:51
kanzuresegments will probably start at 20 bp to 100 bp in size, unlikely to be less than 20 bp10:52
fennyou can use ligase and gibson assembly up to ~10k and then homologous recombination in yeast for larger fragments up to 1M?10:52
kanzuresounds right to me10:52
fenna chromosome is less than 1G10:52
kanzureoh yeah, right, divide by 4610:52
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kanzurefenn: that's like saying that the foxes just finally decided to give up after a few generations, instead of any selective pressure for tameness by not breeding very-not-tame foxes.10:55
fennhttps://en.wikipedia.org/wiki/Mycoplasma_laboratorium#Bacterial_chromosome_synthesis10:56
kanzurei doubt you can find a good argument against directed evolution and iteration itself, however you could have a reasonable argument about "what the actual genetic landscape happens to be"- e.g., the amount of mutation and combinations to test to get a pig that doesn't die from 20 km drop might require more combinations of mutations than we have time left for in lifetime of universe, or something. that would be a valid rebuttal.10:56
kanzurebut v. difficult to guestimate about shape and structure and nature of genetic landscape10:57
kanzurealso makes things hard to decide when to give up on an attempt at evolutionary search over genetic landscape10:58
kanzurebecause for all you know the necessary mutations might be very close in mutation-choice-space....10:58
kanzurei suppose if you know the actual set of problems that cause termination of 20 km dropped pig, then you could figure out whether you feel it's reasonable that simple mutations could effect those results10:59
fennyeah the pig might have really large ears10:59
fennvery strong hoofs10:59
kanzurefor example, bone breaks might cause the death of the pig (among other things!), so better bone density, or shock-absorption bones or something, bone density is easy to imagine a series of simple mutations contributing to, shock-absorption not as easy to imagine....10:59
kanzurebone density easier to imagine because i think we've actually seen dense bone mutations somewhere, not sure where11:00
kanzurei think it was aubrey de grey that was arguing that if you run a steamroller over some pigs and breed the results, you'll just get a bunch of pigs that survive steamrollers. and i was like "yeah? that sounds great to me."11:01
kanzureyou might accidentally get pigs that metamorphize into having a second-stage of life where they are just a blob of meat with broken bones and puncture wounds. but that's technically still survival.11:01
kanzurevarious troubling questions about opportunity cost and when to give up on an evolutionary search attempt for some problem11:03
kanzure"well just limit the search length to some cost less than the saved cost of not having to clean up 20 km dropped pig carcass from street surfaces"11:03
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kanzuretrying to find that old evolutionary search site about TANSTAAFL11:08
kanzureinstead found some thesis about "evolvable virtual machines" https://ourarchive.otago.ac.nz/bitstream/handle/10523/1910/NowostawskiMariusz2008phd.pdf?sequence=311:09
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kanzurehttp://no-free-lunch.org/11:17
kanzuresite is operated by martin sewell <martin@martinsewell.com>11:20
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maakukanzure: interesting find (EVM)12:19
kanzurenatasha vita-more has been posting some emails to extropy-chat upset about the criticism over her cryonics and celegans memory work here https://news.ycombinator.com/item?id=959420112:24
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nmz787_whttp://hackaday.com/2015/10/09/optical-rectenna-converts-light-to-dc/12:55
nmz787_wpretty sweet12:55
nmz787_wwe should find their protocol12:55
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AureliusSorry for nickspam12:58
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nmz787_wstreety: power-wise the lm317 should be fine... the laser itself is probably 100mW or 500mW... who knows, it came from ebay and originally China. From a lithography standpoint, with the laser being focused, it is already much too powerful. As is, and I haven't tried maxing out the feedrate settings on the XY gantry, but it is etching and cutting paper easily... so I'm sure that is about 10 or 100X (or maybe 1000X) too bright f13:05
nmz787_wyou need something like a few mW per sq centimeter I think13:05
kanzureyou have cutoff at "(or maybe 1000X) too bright f"13:06
nmz787_wso focusing a 100mW beam at even 100 microns sq (circular? elliptical? eh figure a square)13:06
archelsnmz787_w: that's output power though, right? what's the input power?13:06
nmz787_w(or maybe 100x) too bright for photoresist13:06
nmz787_w1000X *13:06
nmz787_wsorry, I am on webchat13:07
nmz787_wsurprising it doesn't auto take care of long lines13:07
nmz787_wI mean on webchat.freenode.net13:07
nmz787_warchels: oh, hmm, idk how cheap chinese lasers are marketed13:07
nmz787_wI've usually only heard they're severely under-labelled, so they can get through customs13:07
nmz787_wI can hookup a current meter though this weekend13:08
nmz787_wbut in general, I feel like burning/cutting paper is still 10-1000 times too bright for photoresist13:08
nmz787_wyou only want the molecules to recajigger, not discombobulate13:08
nmz787_w:P13:09
CaptHindsightsounds like post-doc stuff to me13:09
nmz787_wthe jargon?13:10
nmz787_wno, I think that's appalachian13:10
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fennthe c. elegans vitrification paper looks fine13:24
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fenni don't see what being published in a big name journal has to do with the quality of the science13:28
fennyou'd think people would know that, but i guess there are idiots everywhere you look13:28
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Betawolfbig-name journals have a bigger readership and so articles come under more scrutiny (after publication). Smaller journals less so.13:30
BetawolfThis doesn't mean a paper in a smaller publication will be bad science, it means that if it was bad science it'd be more sensible to submit it to a smaller journal.13:31
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fennyou need a montage: http://youtu.be/qJckchby55E13:48
fenn.title13:48
yoleauxPush It to The Limit Petman, Atlas Boston Dynamics - YouTube13:48
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kanzureopenworm videocast-only brain emulation journal club https://plus.google.com/u/0/b/117948341754627144949/events/cv9l18020h2cc0doj62h29errn0?n=114:24
kanzureugh so many videos, so few transcripts (none). how inconsiderate.14:25
kanzure( https://plus.google.com/u/0/+OpenWormOrg/posts )14:25
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maakukanzure fenn : thanks for explaining the DNA printing process. it makes a lot more sense now how it integrates with the broader transhumanist project14:29
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kanzuremaaku: now that cambrian genomics is dead in the water, i think it's up to hplusroadmap to continue their short-term mission of replacing 30-60% of all plant dna on the surface of the planet with synthetic alternatives14:36
kanzurefenn: errors-of-omission are the worst. what's missing on the wiki?14:36
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kanzurehowdy neals15:11
nealssup kanzure15:15
nealsanother busy day in ##hplusroadmap15:15
kanzureelliptic curve stuff is up15:16
nealscool, what are you working on?15:17
kanzurereading libsecp256k115:17
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kanzurere: "100s of millions of drops per second is not correct" should be, 5k nozzles at 20 khz is 100M/sec15:36
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kanzure"genetic landscape" is not an actual term according to wikipedia... what's the one that means "the stuff that evolutionary search is finding out for you"?16:17
nealshttps://en.wikipedia.org/wiki/Evolutionary_landscape ?16:43
streetysounds like the input power for that laser isn't going to be too massive. If it can run on a lower voltage then the lm317 may work fine.16:44
streetyI have a book or two and some course notes on power electronics if it is proving trickier than anticipated16:44
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kanzure"In either case, movement tends to be toward areas of higher fitness, though usually not the global optima."16:46
kanzurewhat?? movements should be capable of going in any direction away from fitness or towards.16:46
kanzure"What exactly constitutes an "evolutionary landscape" is confused in the literature. The term evolutionary landscape is often used interchangeably with adaptive landscape and fitness landscape, though other authors distinguish between them. As discussed below, different authors have different definitions of adaptive and fitness landscapes. Additionally, there is large disagreement whether it should be used as a visual metaphor ...16:47
kanzure... disconnected from the underlying math, a tool for evaluating models of evolution, or a model in and of itself used to generate hypotheses and predictions. Clearly, the field of biology, specifically evolutionary biology and population genetics, needs to come to a consensus of what an evolutionary landscape is and how it should be used."16:47
kanzurerofl16:47
kanzurelet's see what tim schmidt's gang says about this, http://beacon-center.org/blog/2012/10/08/evolution-101-fitness-landscapes/16:48
kanzure"In reality, fitness landscapes are highly dimensional and impossible to visualize"16:49
kanzurejs simulation of fitness landscape stuff http://www.cse.msu.edu/~zamanlui/processingJS/draw_fitness/16:50
kanzurehmm this population doesn't seem to ever grow even if you connect different peaks for the population16:53
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kanzure.title https://www.youtube.com/watch?t=2&v=FTBUIJwlVBg16:59
yoleauxVisualizing coevolution in dynamic fitness landscapes - YouTube16:59
CaptHindsightfenn: 2656 nozzles x 40Khz = 106,240,000 drops per second max for one printhead, crazy but some printers actually achieve >2 Billion drops per second using multiple heads17:00
fenni stand corrected17:06
kanzurethis is an okay one: http://beacon-center.org/blog/2014/04/07/beacon-researchers-at-work-holey-fitness-landscapes/17:06
kanzurei have no idea why nobody has tested >1M drops/sec with a printhead for dna synthesis reasons17:06
CaptHindsighthttp://www.memjet.com/products/labels  is between 100M and 600M drops per second depending on how you count or overlap drops17:07
fenn64k ought to be enough for anybody17:07
CaptHindsightkanzure: the printhead manufacturers don't care, they don't share specs and they want you to spend $100K on your first batch of heads17:08
kanzureif $100k gets me 1 trillion drops/sec then things start getting really interesting17:08
CaptHindsightcloser to 1 billion drops per second17:09
fennit seems like they are just parallelized so meh17:09
CaptHindsightthey wish they could be drug companies17:09
fenntoo many parallelized cooks in the kitchen17:09
CaptHindsightyeah only 4-8 channels/colors/fluids per head17:10
kanzurei think you mean too many parallel turtles all the way down17:10
CaptHindsightmost are 1-2 channels17:10
kanzureare the >1B drops/sec printheads assuming a controlled atmosphere?17:11
kanzureany special pressure/temperature requirements beyond range of consumer inkjets?17:11
CaptHindsight >1B drops/sec printer or printhead array, a single head is ~100M drops per second17:12
CaptHindsightjust out of the wind is all17:13
CaptHindsightand temp is controlled for consistent jetting since the viscosity of the fluid will change over temp17:13
kanzureinkjet controls temp, or is that the responsibility of your junk around it?17:14
CaptHindsightindustrial heads will have built in heaters17:14
kanzurecool17:14
CaptHindsightsome even have microprocessors that adjust the waveform based on head temp17:15
CaptHindsightbuilt into the head17:15
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CaptHindsightbut they don't even share the programming spec for those even under NDA, you might have leave them your liver17:16
kanzurei never wanted a liver anyway, they can have it17:16
CaptHindsightthey change you ~$50K to program those heads for you17:17
kanzure"2 High dimensionality means a large number of genes (loci) or number of nucleotides."17:17
kanzurethis seems like the wrong definition; i thought dimensionality was supposed to be based on selection criteria.17:18
CaptHindsightI mean develop a ~2k bit file for you for the internal eeprom17:18
kanzurehmm they have annual report http://beacon-center.org/wp-content/uploads/2014/10/BEACON2014AnnualReport_Public.pdf17:18
kanzurehm page 6 claims they have insight into the evolution from single cell to multicellular life17:19
kanzureseems to be based on concept of metabolism and metabolic byproduct mutations being poisonous to other processes17:20
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kanzureon page 25 i'm not sure why they think a markov model is an evolutionary search algorithm (they are using a markov model for protein folding predictions)17:25
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kanzurepage 43 mentions some work about dna secretion systems17:30
kanzurethere was a 2013 igem team funded by beacon17:33
kanzurecalling themselves "darwin's bulldogs", evidently17:34
kanzurehod lipson is an adivsor for beacon, and ellington shows up in this doc. hrm.17:36
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kanzuretim schmidt introduced me to someone at beacon back in january (titus brown) but it turns out that titus was someone i met on slashdot in 200717:59
kanzurebut only now realizing this. oops.17:59
kanzurei wonder if there's an equivalent to shocking a heart that works for dying/dead livers, such as those that die before transplanting 'em18:07
kanzureheart and lungs survive 4-6 hours, kidneys up to 36 hours, livers up to 12 hours. damn.18:08
kanzurehttp://www.transweb.org/faq/q24.shtml18:08
kanzurerelevant chart http://www.transweb.org/images/content/faq_q24.gif18:08
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kanzureJawmare: welcome back18:36
Jawmarehi18:36
kanzure21:54 < kanzure> david dalrymple got into that marblestone thesis18:41
kanzure21:54 < kanzure> very sinister18:41
kanzurewas checking my email, turns out dalrymple introduced me to marblestone in 2012... oops. dropped the ball on that one.18:41
kanzureworld is much smaller than i originally anticipated18:44
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kanzure"Dalrymple & Co. LLC is closed for business due to the upcoming holiday on Monday, October 12th. We will resume business at some point and will reply to your request shortly thereafter. [This is an automated message. This is a no-reply address. Please direct further inquiries to support@dalrymple.co.]"18:58
kanzurefriendship is weird18:58
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mgindoes anybody here want to live forever?19:34
drethelinmarblestone?19:48
drethelinmgin: how do you know I'm not already living forever19:48
mginhey19:50
mgincan you unban me from lesswrong19:50
mginlol19:50
mginit's been like a year19:50
drethelindo you mean slatestarcodex?19:51
mginhm?19:51
mginwait wut?19:52
kanzureno, i'm the one you banned from slatestarcodex20:02
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--- Log closed Sat Oct 10 00:00:52 2015

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