2015-10-06.log

--- Log opened Tue Oct 06 00:00:49 2015
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kanzurebeep03:37
justanotheruserbop03:38
kanzuresup03:47
justanotherusertrying to organize my getting stuff done setup03:49
justanotheruseralso trying to get stuff done03:51
kanzurealright03:52
kanzureneutrinos have non-zero mass https://news.ycombinator.com/item?id=1033775504:01
kanzure"Dear readers, This month celebrates the 10 year anniversary of the classic book The Singularity Is Near, written by Ray Kurzweil, published in September 2005"04:06
kanzure.title http://www.nature.com/ncomms/2015/151001/ncomms9414/full/ncomms9414.html04:07
kanzureer.. nevermind. terrible paper.04:08
poppingtonicbeep boop04:26
justanotheruser"Spire is a global nano-satellite powered data platform"04:26
nshBEEEEP04:51
nsh.title http://www.nature.com/nature/journal/vaop/ncurrent/full/nature15263.html04:51
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poppingtonicI like how nature.com links to references with context and links back to the point of the article with the reference. makes it slightly easier to read.05:48
poppingtonicPermacoin05:49
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kanzurenah not permacoin06:07
kanzuredon't bother06:07
justanotheruser"Turning Bitcoin coin making into one big Wayback Machine"06:11
justanotheruserthis should be good06:11
justanotheruser"Permacoins would be generated when users store archival data downloaded from a huge data pool. "06:12
justanotheruserOh man, this sounds verifiable without trust06:12
justanotherusermeh, I'm just preaching to the choir, bye06:12
poppingtonicnamecoin + ipfs?06:15
* kanzure shakes his head06:16
kanzureipfs's filecoin was never going to work06:16
* Taek self promotes Sia06:18
kanzurei'll allow it but only if you promise to include criticism you've received :P06:19
kanzure"Computational Insights and the Theory of Evolution - Dr. Christos Papadimitriou" https://www.youtube.com/watch?v=KP0WFbdHhJM06:19
TaekSia had to be rewritten, it was originally designed as a generalize-storage-for-consensus platform, and was very broken06:20
Taekthe biggest issue with today's platform is host selection - that's left out of the protocol06:22
Taekhttps://github.com/NebulousLabs/Sia06:22
kanzuresomeone should do a non-cryptocurrency-based storage system where people can just arbitrarily join with more random hardware. central service provider treats them like contracted hosting parties. use default legal contract and put them through onboarding process, something somewhat automated. accept even small 1 MB providers.06:23
Taekafter the original Sia was demonstrated to be hopelessly broken, we very nearly picked a centralized model06:24
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kanzure"bioprinter" http://2015.igem.org/Team:TU_Delft/Design06:33
kanzurehttp://2015.igem.org/Results06:33
JayDuggerGood morning, everyone.07:07
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kanzure.title https://news.ycombinator.com/item?id=1033816507:18
yoleauxEugenics, Ready or Not | Hacker News07:18
kanzure"If you want to be pedantic, having sex with people you find attractive is already eugenics." duh?07:18
TaekI think a lot of people miss that point07:19
poppingtonichello JayDugger07:19
kanzureTaek: maybe they just don't have much sex :-)07:20
poppingtonicdid they even mention iterated embryo selection? I mean, the bostrom paper on it describes exactly why someone would want to perform embryo selection, using Tay-Sachs as an example I think.07:21
Taekpoppingtonic: do we know enough about which genes are preferrable to make iterated embryo selection useful?07:22
kanzureiterated embryo selection is so weird; there's no reason to use physical embryos for that.07:23
poppingtonicno. the same requirement for single-generation embryo selection  hasn't even been fully explored yet.07:23
poppingtonicwhatever "fully explored" even means... this is so far out. I don't have references.07:24
TaekI'm 95% sure that's going to be my next startup/profession07:24
kanzureyou can use somatic cell nuclear transfer to avoid all of the other embryo stages07:25
kanzurenot sure why bostrom wasn't informed about this07:25
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Taekif you're referring to his book, he may have thought that to be too much detail - the general concept is close enough to understand what he's getting at07:26
kanzureno i mean the paper. which book?07:26
Taekhe talks about iterated embryo selection in Superintelligence07:27
kanzurealright07:27
poppingtonicI think that's part of the mechanism he *skimmed*07:46
poppingtoniche doesn' t go into too much depth in Superintelligence. "Beyond the scope of this book" is what he might have written07:47
poppingtonicnickbostrom.com/embryo.pdf07:48
Taek40407:52
poppingtonicnickbostrom.com/papers/embryo.pdf07:53
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poppingtonicTaek what does Sia mean? Is it an acronym?08:23
Taeknah, just a phonetic. loosely pulled from: https://en.wikipedia.org/wiki/Sia_%28god%2908:24
fennsuper intelligent acronym08:28
poppingtonicself-indicating acronym08:29
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fenn"Francis Galton had done some early psychometry, and published his results claiming that the English upper class was the upper class because they were genetically superior to the lower classes. This result was widely accepted by both the progressives and the conservatives. The difference between the left and the right was not opposition to the principle of Social Darwinism, but just what should08:53
fennbe done about it. The progressives advocated for eugenics to lift the lower classes from the 'genetic deficit' they were born into, while the traditional conservatives believed that this was unnecessary and that the situation as it existed was the natural order that shouldn't be fixed."08:53
fennhistory can be so embarrassing08:53
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fennanother difference between humans and chimps, smaller jaw muscles: "we all share a defect in the gene that creates a protein called MYH16, a chief component of the powerful jaw muscles of many non-human primates http://www.nature.com/news/2004/040322/full/news040322-9.html09:03
kanzurealso various throat changes that assisted with vocalizations09:04
fenni haven't seen this one discussed much though, or at least i don't remember it09:05
kanzuresee bottom left of page 7 http://diyhpl.us/~bryan/papers2/neuro/language/The%20evolution%20of%20human%20speech%20-%20Lieberman%20-%202007.pdf09:05
fenn"Muscle sculpts bone," he says. "The structure can be modified by the forces acting on it."09:06
fennBy doing away with large anchors for chewing muscles, our skull may have freed itself to grow into its modern, rounded shape, says Stedman. Powerful jaws may be incompatible with powerful brains, he suggests.09:06
nshOn Sex, Evolution, and the Multiplicative Weights Update Algorithm -- http://www.eecs.harvard.edu/econcs/pubs/Meir_aamas15.pdf09:06
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kanzureyes i suppose over time muscle might be more important than bone, so the bone gets pushed around to accomodate the useful muscle09:09
kanzure(not in a single individual's lifetime)09:09
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fennno he means the muscle literally pushes the bone around during development09:10
fennwith mechanical forces09:10
fennfig 3 in that lieberman paper is interesting; i didn't realized the clustering of vowels was so clean and symmetrical09:11
fennrealize*09:11
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poppingtonicOne thing I got from fenn's Galton quote is to place very little trust in the current time-slice of civilization's notion of "that which is good and should be promoted", if it is not evidence-based.09:23
kanzurehow about "party lines are nonsense"?09:24
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poppingtonicTaek: from the paper: "Standard practice today involves the creation of fewer than 10 embryos. Selection among greater09:30
poppingtonicnumbers than that would require multiple IVF cycles, which is expensive and burdensome. 1-in-1009:30
poppingtonicselection may thus represent an upper limit of what would currently be practically feasible. New09:30
poppingtonictechniques for maturing eggs in vitro might make the creation of more embryos feasible, though with09:30
poppingtonicdiminishing returns.09:30
poppingtonic"09:30
fennagain, we can do much better than just selection09:31
fennhere's a bunch of low hanging fruit http://diyhpl.us/wiki/genetic-modifications/09:31
poppingtonickanzure: that too09:31
kanzure"maturing eggs in vitro" is skippable.. why bother going to eggs when you can just setup the problem better?09:33
* fenn looks around for erasmus09:33
fennbecause cloning is bad mmkay09:34
kanzurei mean yes it's useful to mature eggs in vitro. sure. but the point was to.. er.09:34
kanzureoh is that the problem?09:34
poppingtonicthese are very cool fenn09:34
poppingtonicthanks09:34
poppingtonicthe fruits, i mean ;)09:34
poppingtonicThe lactase persistence section mentions that other SNPs are predictive but doesn't mention which ones.09:35
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fennalso we can directly correct undesirable mutations with TALENs, CRISPR, zinc finger nucleases, and many other gene therapy vectors and site-directed mutagenesis schemes09:37
fenninstead of waiting around for the mutation to magically fix itself and select for it09:37
fenngenetics is pretty boring so far because nobody does experiments on things that matter09:39
fennthis is why we have to go dig up bodies of dead nobel prize winners09:39
fennalso people with musical talent, good looks, historical political figures, etc09:40
kanzureyes the focus on pathologies-only in science is very weird09:41
fennsome of these factors will turn out to be epigenetic and won't show up in their descendants, nevermind the difficulties of figuring out which genes are important only from descendants09:42
fennthere should be a "notable people who had this SNP" section on every page in SNPedia09:43
kanzuremutantpedia?09:43
fennis that a thing?09:44
kanzureno :-(09:44
kanzurebut there is an x-men wiki09:45
fenni feel gross saying it, but there's a lot of room for branding and marketing in genetic alterations09:45
fenn"a study of 400 individuals" is not a captivating narrative09:45
fennyou have to talk to people at their level; intelligence increasing modifications won't become widely popular if it involves reading statistical studies in scientific journals09:47
kanzurei don't think that intelligence increase is necessarily the best way to frame it anyway09:47
kanzure"better language acquisition" has been my go-to recently09:47
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fennplease elaborate09:48
FourFirefenn, or they will, but only amongst academic elites09:48
fennFourFire: exactly the people who don't need these modifications09:48
kanzurespeaking multiple languages is often deemed a sign of intelligence. but also it's a practical and useful skill.09:48
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kanzurewould be nice to demonstrate minimal exposure to multiple languages and somewhat adequate verbal skills in each09:49
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FourFirewell I wouldn't say "don't need", but yeah, others will need them more09:49
fennenglish is obliterating native languages all over the world anyway..09:49
fenni guess you could market it to non-english countries as "your baby will be fluent in english by age 2!"09:50
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fennUSA will probably ban genetic modifications soon enough09:50
fennif not already09:51
kanzureright after they ban sex, amirite?09:51
fennpretty sure it's illegal09:51
fennbabies come from the stork09:51
FourFireheh, anyone who's rich enough will just travel another country to do the gene therapy09:52
kanzurethere's a certain subgroup that i think could be trivially marketed to09:52
fennagain, the people who don't "need" it09:52
FourFire^09:52
kanzureespecially for muscle development and intelligence09:52
FourFire^09:52
fennwhat?09:52
kanzurenevermind09:52
kanzureit's the same group that is super interested in surrogacy heh09:53
FourFirekanzure, you really feel annoyed by them, don't you?09:53
kanzurewho?09:53
FourFireoh no I guessed wrong.09:53
FourFireyeah that too09:53
fennfourfire try forming complete thoughts and writing them out09:53
FourFirefunny, I was told that back when I joined that other channel09:54
fenni'm just trying to fix some kind of communications breakdown here09:55
FourFireI assumed kanzure was referring to silicon valley nerd types, which overlaps substantially with Lesswrong,09:55
fennoh09:55
FourFirebut he is actually referring to transpersons09:55
poppingtonictoo true.. that's what i thought09:55
FourFire(which also has an odd overlap with LW)09:55
fennafaict the lesswrong people are not really interested in having children, i may be wrong though09:56
fenntoo busy saving the world or whatever09:56
kanzureno i was not talking about transpersons09:56
kanzureand i was not talking about nerd types09:56
FourFireyeah, I said it, I guessed wrong.09:56
fennwhat sort of person is interested in surrogacy?09:56
FourFirea female without the equipment09:56
kanzureinternet masculinity subculture :P09:56
fenni only know one and he's an outlier09:57
FourFiretranspersons are outliers09:57
kanzurethere's not enough of them anyway09:57
fenni guess, it's pretty rare but not genius-level rare09:57
fenni think i read 0.2%-0.5%09:57
FourFireyeah and in LW it's more like 1.5%09:57
fennbah impossible to get reliable statistics from the internet10:01
drethelinlots of people in china want surrogates apparently10:01
drethelinto sneak around some of the 1 child laws?10:01
kanzurehow about to sneak around 9 months of shit?10:01
kanzure*9 months of feeling like shit?10:01
fenni thought they changed that law recently10:01
drethelinwell that too10:01
fennhttps://en.wikipedia.org/wiki/One-child_policy#Relaxation_of_policy10:02
fenn"Under the new policy, families can have two children if one parent is an only child."10:02
kanzure"oops we waited so long that families missed their fertility window, bwahaha"10:03
fennchina's policy is inherently eugenic because it encourages people to plan out when and how to have children, rather than just whatever happens10:04
fennthe gender ratio imbalance is evidence of this, i guess.10:05
fennno takers huh10:12
fenn<- bad troll10:12
fenn"families with children with disabilities have different policies and families whose first child suffers from physical disability, mental illness, or intellectual disability are allowed to have more children"10:15
fenn"In most areas, families are allowed to apply to have a second child if their first-born is a daughter"10:15
kanzurebad idea10:15
fennyeah nobody ever mentioned that tidbit10:15
fennthat would lead to 50% more males even without any intervention, right?10:16
fennor 25%10:17
kanzuream i still confused about the physical number of dna molecules per human cell?10:17
fenn4610:17
fennunless you have down's syndrome or something10:18
kanzurebut.. plasmids?10:18
fennhumans don't have plasmids10:18
Taek"...there's a lot of room for branding and marketing in genetic alterations" - Genes by Dr. Dre10:21
fennyes, you too could have dr. dre as a child...10:21
xrrI ate 100 mg vitamin E for 70 days. Achieved nothing: http://oi58.tinypic.com/70ax74.jpg10:22
fenni wonder if there is a celebrity sperm bank10:22
@maakuone child policy was never uniformally applied10:22
@maakuit was always a matter of kickbacks to the local party official10:22
fennmy new favorite insect https://en.wikipedia.org/wiki/File:Myrmecia_pilosula_specimen_mandibles.jpg10:26
Taekfenn: mathematical mistake. If every parent adopts the strategy of stopping at the first male child, you still end up with 50% males and females.10:26
kanzurei don't think those mandibles can close10:26
fennfemale jack jumper ants (myrmecia pilosula) have 2 chromosomes; males have 1 chromosome10:27
fenn"They prey on small insects and use their barbless stinger to kill other insects by with injecting venom."10:28
kanzurewhat were the things you wanted to do with super-sized insects, again?10:28
kanzuresomething about food, but some other stuff i forget too?10:29
fennTRY AND TAKE OVER THE WORLD10:29
kanzureyes because the super-sized wasps are going to construct human-habitable hexagonal living facilities everywhere, sure.10:30
fennyou are catching on to my schemes10:30
kanzureiirc partly it was just a (very reasonable) "it will be awesome, come on"10:31
fenni am embarrassed you even have to ask10:32
fennhttp://chronicle.augusta.com/sites/default/files/imagecache/superphoto/12760807.jpg10:32
fennhttps://s-media-cache-ak0.pinimg.com/236x/ca/a5/fd/caa5fd5c3fc6996a9c49ea3e71996cea.jpg10:35
fennthe possibilities are endless10:36
TaekI imagine that you could learn a lot about favorable genes by applying massive amounts of machine learning, but you'd probably need 10^7-10^9 datapoints according to my early research10:40
fennhttp://fennetic.net/irc/135_Daruma%21_ID1-Monochrome_Section_Art_7.jpg wasps could be selected for physical size and adaptability to implanted cybernetic control systems10:43
fennthis is from intron depot 110:44
fennoh urlcodes in filenames are bad10:45
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fennsomehow i have failed to find lots of dinotopia-like images of humans and giant insects whimsically living in harmony10:54
@maakuNausicaä10:55
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fennyeh i'm thinking like a giant rhinoceros beetle pulling a plough10:56
delinquentmeooh fenn10:57
delinquentmei have pics for yew10:57
fennhexagons or gtfo10:57
delinquentmecould you settle for triangles?10:58
fennyes10:58
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fennhttp://animemiz.files.wordpress.com/2009/01/nausicaa3.jpg10:59
kanzurewtf happened to that r2d2 unit?11:00
fennthe girl is clearly genetically engineered, note the enormous cranium11:00
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delinquentmehttp://imgur.com/gVZaVba11:02
delinquentmethere we go11:02
delinquentmeit was cool11:02
delinquentmeit was big11:02
delinquentmeand it gets bigger11:02
fennis this alex iglesias' thing11:03
fenni only see one triangle11:04
fenngrr stupid time portals11:06
kanzurewhy giant wasps instead of giant cybernetic eagles?11:07
fenneagles are picky and not easily programmable11:07
kanzurehttp://rs1img.memecdn.com/planet-hopper_c_1672593.jpg11:10
kanzuredelinquentme: ^11:10
kanzureah, better version http://www.prikol.ru/wp-content/gallery/june-2013/podborka-28062013-33.jpg11:10
delinquentmehah wow. . yes definitely death metal cricket11:11
delinquentmefenn, thats the giant mech / robot thats residing here in oakland11:11
delinquentmeyou've seen the america vas japan robot fight right?11:11
kanzure"heavier than a sparrow"11:13
fenni've seen some name-calling on twitter but not much else11:14
kanzuredeinacrida heteracantha, titanus giganteus, megasoma elephas elephas, megasoma actaeon, goliathus goliatus11:16
fenninteresting that IHMC is collaborating on the giant robot battle11:23
fenn"you have a choice: watch another cat video on youtube, or make your childhood dreams come true. what's it gonna be?"11:29
fennthat's not the most motivating thing they could have said11:29
delinquentmefenn, i guess that means i like cats more than you do11:30
fennis this mark 1 robot at nimby?11:30
kanzureweird that the wiki doesn't have "biologically-plausible things that nature hasn't entirely stumbled into yet"11:32
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kanzureor, rather, "biologically-plausible that nature hasn't had good reason to consistently select"11:33
kanzurenot sure where to source that sort of material from. orion's arm isn't quite the right source.11:35
fennthere's some stuff in http://diyhpl.us/wiki/human-modifications.csv but not nearly enough11:35
kanzureyeah we should get better at documenting potential human genetic alterations. including gene+cybernetic modifications. or other combinations of things.11:36
kanzure"we should drop pigs from airplanes and select the ones that survive"11:38
fennyou would get bouncing pigs, not flying pigs11:38
kanzurewasn't aiming for a flying pig11:38
kanzurejust pigs that don't explode on impact11:38
fennok then. hogs away!11:38
fennin general i'm still skeptical of the "throw a bunch of pigs at the wall and see what sticks" approach11:39
fennsurely there are more efficient search strategies11:40
kanzurewell, genetic engineering helps, but bruteforce is surprisingly effective over the past few billion years11:41
fenni hope the error in that statement becomes obvious11:42
kanzurehumans produce a few billion years per year11:42
delinquentmefenn, its this robot : http://www.cnn.com/2015/07/07/tech/giant-robot-fight-challenge-accepted/11:46
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fennkanzure what about just selecting for giant insects? it should be easy right?11:56
fennthe test is very objective, just the total body mass11:57
kanzuresure. but i still need reminders about the motivations here, besides being awesome.11:57
fennyou could optimize your selection strategy11:58
fennthen use that strategy on other dimensions11:58
fennlike intelligence or whatever, where it isn't so easy to measure11:58
kanzureno no i mean.. iirc there was something about "grow giant crickets instead of cows, cricket meat is more efficient" or something.11:58
fennmeh11:58
fennsmaller crickets would be more efficient i think11:59
kanzureas for cybernetics- not sure, i guess you could have flying machines that last more than 10-30 minutes, which would be nice.11:59
fenneconomics, it should be way cheaper to grow a wasp than to build a flying robot12:00
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kanzurestill needs all the electronics12:00
kanzurei think you need cheaper than feeding a flying robot12:00
kanzure*you mean12:00
fenn.wik darpa cyborg beetle12:00
yoleaux"A cyborg (short for "cybernetic organism") is a being with both organic and biomechatronic parts. The term was coined in 1960 by Manfred Clynes and Nathan S. Kline. D." — https://en.wikipedia.org/wiki/Cyborg12:00
fenndammit12:00
delinquentmealso .. next year. I'm thinking about presenting my xenozoonosis hack at deacon12:03
delinquentmedefcon*12:03
delinquentmeanyone want to go on stage w me?12:03
fennbriefly, what is your hack?12:05
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fenn.title http://www.technovelgy.com/ct/Science-Fiction-News.asp?NewsNum=142112:09
yoleauxHI-MEMS: Control Circuits Embedded In Pupal Stage Successfully: Science Fiction in the News12:09
fennRead more about Roachsters, full-size anthropod-based vehicles with embedded control structures from Easton's 1990 book Sparrowhawk.12:09
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fennheh they have wheels12:11
fennand spinal cords :\12:11
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kanzurecould be new line of hotwheels12:32
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kanzure"hello, welcome to the future, please take your flying car and gtfo"12:39
kanzuregah was bit for multiple days debugging that importaddress rescan=True is the default12:40
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kanzurejustanotheruser: part of the magic is to pick good tasks with high leverage. doing a million tasks is useless if the tasks are poor quality (even if the quality of the tasks performed is high-quality).13:20
kanzure*quality of the work performed is high-quality)13:20
kanzurealthough if you become too discerning about task quality then you turn into jrayhawk13:22
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jrayhawkthe causation probably goes both ways13:38
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kanzurere: lack of evidence of stars being moved https://news.ycombinator.com/item?id=1025222214:35
kanzure"If binary star systems were systems in which stars were moved into the system, we should see evidence of stars being moved and consumed. I have also read about stars being created (e.g., starting a fusion process with all the hydrogen and helium in Jupiter, Saturn, etc.)."14:35
kanzure"There is currently no evidence which suggests stars are being moved. We should see either large gravitational tugs or engines such as Shkadov thrusters. The latter should be plainly visible. The former should be easily detected by extrasolar planet detection methods. Unless the tugs are spherical, the light curves of the tugs would definitely pique interest. In any case, moving a star seems a rather extreme and expensive measure. It is ...14:35
kanzure... probably more effective to consume the star onsite and use the energy locally or send only the energy back."14:35
kanzure"There seems to be no evidence of stars being consumed, either. Dyson spheres (or swarms) have actually been searched for locally by comparing visible and infrared wavelengths over sections of the sky. None have been found. Intergalactic searches have also been done by looking for galaxies which glow too brightly in the far infrared. No luck."14:35
kanzure"It is not just a question of a mistaken belief that the artificial is natural. The properties of light are the same here on Earth as they are billions of light years away. Further, for all those galaxies and stars to be engineered in the same way aross billions of light years (with some points being unable to communicate with others since the Big Bang), is all but impossible. Life would have to evolve at effectively the same rate and ...14:35
kanzure... come up with the same solutions in all those hundreds of billions of galaxies (and yet somehow be different here in the Milky Way). Given the variety of life on Earth and the variety of solutions it has evolved, that seems unlikely."14:35
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kanzurehttp://www.theguardian.com/science/head-quarters/2015/oct/05/whats-the-deal-with-modafinil-nootropic-cognitive-enhancer15:34
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fennwhy would thrusters be visible? a good thruster sends the exhaust particles in a line16:01
fenneven a partial dyson sphere of perfectly flat mirrors would be almost invisible16:02
@maakuexcept for the heat signature16:04
fennthat's not really "plainly visible"16:04
@maakuagreed; i don't think adequate looking has been done16:05
@maakubut then I'd also expect any space faring intelligence that came from natural evolution to rapidly expand into the cosmos at near the speed of light16:06
@maakuso the fact that we don't see them isn't very interesting16:06
fenn2015-08-01.log:04:02 < fenn> "some of the more interesting SETI signal candidates (such as SHGb02+14a) appear to emanate from interstellar space rather than a star" https://entersingularity.wordpress.com/2014/06/10/dark-extraterrestrial-intelligence/   an essay about the implications of thermal noise on the probable location of computronium16:09
fennbasically he says that you should expect to find advanced civilizations far out in the middle of nowhere, away from unpredictable noise sources16:09
fennbecause computers work better at low temperatures16:09
@maakupresent computers do..16:11
fennit's kinda funny because the "zones of intelligence" idea was a purely literary plot device16:13
mgin...16:14
fenn...16:14
mginwouldn't you expect large energy sources where a computronium is16:14
fennread the article16:14
mginbut probably no emissions16:14
mginor little16:14
@maakumgin: you would not expect energy emissions near a resource-optimizing intelligence16:15
mginright16:15
mginwell16:15
mginexcept it's probably going to try to expand in every direction as fast as possible16:15
mginare any of you guys in school16:19
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kanzurewe are all far too cool for school16:42
mginreally?16:43
kanzureapproximately!16:43
mginwhere does one find interesting people to talk to16:43
kanzuredunno, i just send lots of bookmarks to people by email until they become a friend16:45
mginwhat people?16:47
kanzurehttp://heybryan.org/mac.html16:47
kanzurei wonder what orion's arm says about computronium anyway, http://www.orionsarm.com/eg-article/4637faafa643716:57
kanzurehuh, not much16:58
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kanzurehttps://www.reddit.com/r/starwarsspeculation/comments/3nndso/pitch_an_anthology_film/17:51
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kanzurewrldpc1: welcome back18:14
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maakumgin: in school? try clubs18:48
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mginno18:54
caterni try to pretend to be a grad student at my university18:56
caternundergrads are boring18:56
catern(including me)18:56
mginyou're an undergrad?18:56
mginwhat are you studying?18:56
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Jawmareoh hi, this channel looks interesting19:04
Jawmareheard you guys need chemists?19:05
caternmgin: computer science19:07
catern(formerly economics, but the undergrads were too boring)19:07
fennhello chemist person19:07
fennJawmare: what sort of chemistry do you do?19:15
Jawmarestill an undergrad19:16
fenn"try to pretend to be a grad student"19:16
Jawmarebut most of my interest is in organic/inorganic synthesis19:16
Jawmareand some experimental pchem19:17
mginis anyone post grad19:18
fennwe have some problems choosing linkers and solvents for DNA synthesis19:18
mginwhat is life19:18
fenni'm afraid most of that context is swapped out at the moment for me19:19
caternfenn: yes? what's wrong with pretending to be a grad student?19:21
fennoh, i was giving advice19:21
caternmgin: good channel to ask19:21
fenn"don't be boring. sit, stay. good boy."19:21
mgin?19:22
mginare there any other channels19:22
Jawmarebiochemistry19:22
fennlife is DNA and RNA in a phospholipid bilayer membrane19:22
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kanzureJawmare: we are doing dna synthesis using phosphoramidite method (or some other better method if necessary)19:29
kanzureJawmare: http://diyhpl.us/wiki/dna/synthesis/notes/19:29
kanzureJawmare: giant machine can be built, but want to have someone around to help tweak the chemistry and machine to be chemical-compatible with uh.. reality.19:30
Jawmarewhats wrong with DMAP?19:33
Jawmare(except it is very toxic)19:33
kanzuredwho?19:33
kanzure.wik 4-Dimethylaminopyridine19:33
Jawmare3. Capping mixture of acetic anhydride and 1-methylimidazole (or less often, DMAP) as catalysts19:33
yoleaux"4-Dimethylaminopyridine (DMAP) is a derivative of pyridine with the chemical formula (CH3)2NC5H4N. This colourless solid is of interest because it is more than 10,000x more basic than pyridine, owing to the inductive effect of the NMe2 substituent." — https://en.wikipedia.org/wiki/4-Dimethylaminopyridine19:33
kanzurei think because of simplicity of acquiring anhydride19:34
kanzurebut---- dna synthesis is also sorta cargo cult, so if there's better ways, then we should do the better things19:34
* fenn bangs coconuts together19:34
Jawmareother than that, there is not a lot of improvement I can see19:40
kanzurewell, improveents aren't necessary- but there are important chemistry details to this that i'm 100% sure that i don't know about19:41
kanzureduring design and operation of the machine itself, the expertise of someone more familiar with chemistry than i am would be very useful (my background is actually pokemon training, so what the shit does that say?)19:42
fennas a potential lab monkey i'm quite concerned about toxicity19:42
fennthere is literally no information on the safety of DNA synthesis byproducts and reagents19:42
Jawmarebut machine doesn't die from toxicity19:42
Jawmaremsds sheet19:42
fennno information in the msds19:42
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fennjust says it's not explosive or whatever19:42
Jawmareall the reagents have msds sheet19:43
fennbut will i die of cancer in 3 years?19:43
kanzureplus there's lots of obvious chemistry things that are non-obvious to us... this is why we need an extra person. or two.19:43
JawmareDid you guys attempt to do the reaction before?19:44
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kanzurenope, although i did purchase an old and busted dna synthesizer (it's missing a single tube)- just for laughs, reverse engineering, etc.19:45
Jawmareor are there people who did the same reaction before and have paper describing how they attempt it?19:45
kanzurehttps://www.takeitapart.com/guide/9419:45
kanzurethere are some papers but lots of steps are missing19:45
kanzurethese are the sorts of papers that assume prior knowledge19:45
kanzurehttp://diyhpl.us/~bryan/papers2/DNA/abi391/19:45
Jawmare I mean the reaction itself, with beaker, rounded bottom etc19:46
kanzurehttp://diyhpl.us/~bryan/papers2/DNA/POSaM:%20a%20fast,%20flexible,%20open-source,%20inkjet%20oligonucleotide%20synthesizer%20and%20microarrayer.pdf19:46
kanzureyes here is an old paper describing manual approach,19:46
kanzurehttp://diyhpl.us/~bryan/papers2/DNA/Syringe%20method%20for%20stepwise%20chemical%20synthesis%20of%20oligonucleotides.pdf19:46
kanzurereally old versions of the reaction chemistry are described here http://diyhpl.us/wiki/dna/dna-synthesis.html19:46
Jawmareand if you need any papers, just fill this : https://docs.google.com/forms/d/1l9G5TDDwNJrm5QDbNPw7vE7jDaAXwPYC5s_olnvzBQs/viewform19:47
JawmareI have access to most of the journals19:47
kanzuremuch appreciated, we used to run paperbot which would receive requests over irc for papers and then automatically grab 'em https://github.com/kanzure/paperbot19:48
JawmareSo first thing is to replicate the manual apporach19:48
kanzure(at the moment paperbot is out of commission because of a few bugs)19:48
fennhttps://azcobiotech.com/cepa-bulk-dg-ibu-20-8110.html can't find msds now sigh19:48
Jawmaresee if you can get the same result doing it by hand19:48
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kanzureyeah i would be willing to pay someone to do manual approach and document everything, including materials, yields, glassware quality, etc.19:49
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Jawmarehttp://eng.bioneer.com/literatures/msds/Reagents_MSDS/dG%28Ib%29-CE%20%20Phosphoramidite.pdf19:50
Jawmarethats the msds19:50
Jawmare(If it is not availiable on the internet, usually a email to sales will get to the msds, even if you didn't buy it from them)19:53
kanzurei suspect it's the solvents that fenn should be more concerned about :-)19:54
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fennthe 3-methoxypropionitrile sounded concerning19:55
Jawmarehttp://www.sigmaaldrich.com/MSDS/MSDS/PleaseWaitMSDSPage.do?language=&country=CA&brand=ALDRICH&productNumber=65290&PageToGoToURL=http://www.sigmaaldrich.com/catalog/product/aldrich/65290?lang=en&region=CA19:55
Jawmareits on aldrich19:55
Jawmare(the first thing you search for msds is from aldrich19:55
fennanyway like i said my context is swapped out and it's past bedtime19:56
kanzureseeya19:56
fenn"to the best of our knowledge ... toxicological properties have not been thoroughly investigated."19:58
fenn"do not snort the powder, you crack monkey."19:59
kanzurearen't they supposed to import toxology data from similar compounds' msds?19:59
Jawmare?19:59
kanzurewell it's not like we don't know anything19:59
kanzureusually strongly acidic families of chemicals are going to be strongly acidic19:59
fenni'm not worried about acidity20:00
kanzurei was just exampling20:00
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kanzurefrom kahless, through kahless, into kahless we fly20:15
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delinquentme"For all temperatures and salt concentrations employed in present study, base-stacking is the main stabilizing factor in the DNA double helix. A•T pairing is always destabilizing and G•C pairing contributes almost no stabilization. Base-stacking interaction dominates not only in the duplex overall stability but also significantly contributes into the dependence of the duplex stability on its sequence."20:22
delinquentmehttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC1360284/20:22
kanzure.title20:23
yoleauxBase-stacking and base-pairing contributions into thermal stability of the DNA double helix20:23
kanzureguess i had that coming20:23
delinquentmeIm researching the energy involved in the bonds20:23
delinquentmeit also just helped me realize that proximity... but also the rotational position20:24
delinquentmematter in this kind of process20:24
delinquentmeweh.20:24
delinquentmemakes me wonder if i had the DNA free floating in a nanotube ... if it would rotate to meet the other strand when brought into sufficient proximity20:25
kanzurecarbon nanotubes are not solid surfaces20:26
delinquentmetrue20:27
delinquentmebut the same question applies to any nanotube20:28
Jawmaredelinquentme, you can use computational calculation20:33
delinquentmekanzure, would nano engineer be something useful for this?20:34
delinquentmelike Jawmare suggested?  ... i suppose I could do these calls by hand but maybe theres a better way20:34
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wrldpc1ty22:21
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wrldpc1touched on skdb in a recent podcast22:22
wrldpc1would love to have you and/or ben on to discuss in greater detail sometime22:22
wrldpc1https://soundcloud.com/getbusypodcast/5-dangerous-populists-entrepreneurial-scientists-group-openecology-skdb-cloning22:23
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