2014-11-10.log

--- Log opened Mon Nov 10 00:00:46 2014
jrayhawkthis is also the central problem with e.g. nutrition and medical research. when allowed to norm on states of pathology, you can make basically anything look pathological or beneficial.00:01
jrayhawkthough for humans that's s/mutants/epimutants/00:02
fenni'd rather have research done on animals in situations similar to our own than impossibly ideal environments that don't reflect the experience of the majority of humans00:08
fennwe can revise the research later once we figure out how to get people in "non pathological" situations00:09
fennthere was some rat utopia experiment that showed rats wouldn't get addicted to heroin in an ideal environment, but rats (and humans) still get addicted to heroin00:11
fenn...in "the real world"00:12
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fennin the late 1970s by Canadian Psychologist Bruce Alexander built a rat colony (Rat Park), which was 200 times the size of a normal laboratory cage, which housed between 16 - 20 rats of both sexes.he rats in Rat Park, who had wheels and fluffy balls to entertain them, given the option of water or a sweetened morphine solution mostly abstained from the drug. The rats in Rat Park had previously been00:23
fennadministered only morphine hydrochloride for 57 consecutive days in a laboratory cage however once in a less distressing environment they still did not continue consuming the opioid solution. Subsequent experiments where rats were kept in cold cramped cages showed that they were far more likely to consume the morphine solution than the rats in Rat Park.00:23
jrayhawkpeople working from sane null hypothesis jump ahead of the science by decades00:26
jrayhawkhypotheses00:27
jrayhawke.g. weston price characterized menaquinones back in the 1940s, fifty years before everyone else. Roman Shatin worked out mechanisms for epithelial failure causing autoimmunity back in the 1960's.00:32
fennbut weston price had to trek all over the world just to find the mythical humans living in utopia00:38
jrayhawkAyup, he worked hard to find the highest quality null hypothesis available to him.00:40
jrayhawkAnd it's a crying shame more people didn't steal his fine work.00:40
fennhe was a bit out of his field... nutrition/biochem vs dentistry00:41
jrayhawkAnthropology is even further out.00:41
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jrayhawkIt's nice that universities are getting EvoS programs for this sort of thing.00:43
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fennwhat does EvoS stand for?00:48
jrayhawkEvolutionary Studies; a departmental cross-pollination effort.00:49
jrayhawk"multidisciplinary" i guess is the usual term00:49
fennso uh, can we assume that biology is a discipline which already takes evolution into account?00:51
jrayhawkNot usually.00:51
fennthen i don't know what the hell you're talking about00:51
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fennevolution.binghamton.edu/evos/ also does a really bad job of explaining itself00:52
fenn"Instead of challenging the support that evolutionary theory lent to [Social Darwinism], the theory as a whole became off-limits for many human-related disciplines during most of the 20th century."00:58
fenn"Virtually every human-related subject is now being approached from an evolutionary perspective—not only subjects typically associated with science, such as psychology and economics, but also subjects associated with the humanities, such as philosophy, literature, art, history, and religion."01:00
fennhah good luck with that01:00
jrayhawkeven now it's very hard for researchers to discuss group selectionism01:01
fennbecause group selection has been proven not to exist?01:01
fenn(is "group selectionism" the same thing as "group selection"?)01:02
jrayhawkno, there's just immense political pressure to pretend so.01:02
jrayhawkhttp://www.christopherxjjensen.com/2010/10/13/robert-trivers-and-colleagues-on-nowak-tarnita-and-wilsons-the-evolution-of-eusociality/01:02
jrayhawksortof how like lamarckianism was disproven right up until it wasn't01:03
fennhmm.. kin selection is one of those philosophical "identity" questions that will never be resolved01:03
fennoh jeez now you're saying lamarckian evolution is true?01:04
fennbecause of epimutations or something?01:04
jrayhawkexplain to me how "epigenetics" is different from "lamarckian evolution"01:05
fennlamarckian evolution is theoretically responsible for speciation, and epigenetics is not01:05
jrayhawkhow would you test that01:05
jrayhawkactually that's just a stupid line of questioning; speciation is really poorly defined01:06
fennput a species in difficult situation and see if the adapted ones become a new species and the unadapted ones stay the same species01:07
fennbleh i'm no evolutionary theorist01:07
* fenn reads on lamarckism01:08
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fenn"Neo-Lamarckism is a theory of inheritance based on a modification and extension of Lamarckism, essentially maintaining the principle that genetic changes can be influenced and directed by environmental factors.01:12
* fenn is reminded of trying to choke a balloon01:13
fennThe identification of Lamarckism with the inheritance of acquired characteristics is regarded by some as an artifact of the subsequent history of evolutionary thought, repeated in textbooks without analysis. Stephen Jay Gould wrote that late 19th century evolutionists "re-read Lamarck, cast aside the guts of it ... and elevated one aspect of the mechanics - inheritance of acquired characters - to01:13
fenna central focus it never had for Lamarck himself."01:14
fennExamples of what is traditionally called "Lamarckism" would include:01:15
fennGiraffes stretching their necks to reach leaves high in trees (especially Acacias), strengthen and gradually lengthen their necks. These giraffes have offspring with slightly longer necks01:15
fennare you seriously equating this with epigenetics?01:15
Viper168it's more a mutation happens that ends up giving some a longer neck, and those reproduce better01:17
Viper168the mutation happens irrelevant of need, if it gets spread though depends on the situation01:18
Viper168depending on of it's helpful or harmful01:18
Viper168epigenetic changes can be influenced by the environment though01:19
Viper168like the layer that controls how and if genes are expressed01:19
fennViper168: that is neo-darwinism, not what we are talking about atm01:19
fennjrayhawk: it's sort of like, you can say that the complex and nuanced interactions between systems of genes and their environment can be considered a sort of "intelligence" and therefore saying "see, intelligent design was right all along"01:22
Viper168I've seen no evidence genes can be directly altered by the environment01:23
jrayhawkhahaha01:23
fennbut what they really meant is "there's a big old guy on a cloud who thought real hard and magically *poof* life"01:25
jrayhawkwelp, have fun interpreting everything in the least charitable way possible01:26
fennand the lamarckians really meant that the fat man had fat kids01:26
fennsorry was i wrong about how creationists see things?01:26
jrayhawkchrist, it's like i am being dragged back into a discussion with nmz01:27
jrayhawkViper168: I know you'll forget this just like you've forgotten the last several times I have pointed it out to you, but go look up 5-methyl-cytosine and 5-hydroxy-methyl-cytosine01:29
jrayhawkthere's actually a total of eight human nucleotides, but i forget what the last two are and we don't really know what they do anyway01:30
jrayhawks/eight/at least eight/01:30
fennacetyl-?01:30
Viper168it seems you're thinking of the wrong person01:31
jrayhawkno01:31
Viper168because we have only rarely talked01:31
Viper168and certainly not that often about genetics01:31
jrayhawki think the fact that i am willing to try to talk to you is the only reason kanzure hasn't banned you01:32
jrayhawkhis motivations are hard to follow, though01:32
fenni was thinking of histone acetylation, nevermind01:34
Viper168you're tripping01:34
Viper168what have you been smoking01:35
ebowdenWait, did someone here think Lamarckism and epigenetics are the same thing?01:36
Viper168no01:37
jrayhawkyes01:37
fenni see you guys talking about fats and roid rage, but nothing ban-worthy01:37
fenn(in the logs)01:37
Viper168someone mistakenly thought someone did01:37
ebowdenI remember when I saw a creationist I knew of log into the biology channel and I was like "nooooooooooooooooooO!".01:39
Viper168it's worse when you knew them before they went insane01:40
ebowdenLOL01:40
Viper168when someone just decides to adopt it01:40
ebowdenDamn.01:40
Viper168just had an old friend do that, it's weird01:40
Viper168now all of his posts online are about jesus01:40
ebowdenIs that old friend a scientist?01:40
ebowdenLOL01:40
Viper168if he were much of a scientist, he'd not be making wild assumptions01:41
Viper168but no01:41
Viper168he worked on/stole cars in his past01:41
ebowdenLOL01:41
ebowdenSounds about right.01:41
ebowdenDid this guy give you creationist propaganda for your birthday?01:42
Viper168it was only in the last few weeks that he went crazy with it01:42
ebowdenAh.01:43
ebowdenWoah.01:43
ebowdenI've been trying to find someone else who has someone that gives them creationist propaganda for their birthday.01:44
Viper168lol01:44
ebowdenIt seems only me and my brother have that problem.01:44
Viper168there are these people that try to pass it out on weekends here at a popular intersection01:44
Viper168in such instances, I accept satanism as temporarily acceptable to promote01:45
fennebowden: do you come from a strongly religious community? if so how did you escape, or if not how did your brother become a creationist?01:45
Viper168give them a hail satan as I drive by01:45
Viper168I thought about pretending to be with them and help, but have my own pamphlets printed out with something crazy01:46
Viper168and pass those out instead01:46
ebowdenViper168: Imagine those people, but they're your brother-in-law, and the pamphlets are supposed to be your birthday presents.01:46
Viper168by crazy, i mean crazy in a way that isn;t familiar to people01:46
ebowdenfenn: Brother in law.01:46
ebowdenNot my twin brother.01:47
ebowdenJust my creepy brother-in-law.01:47
Viper168lol, that would be nice and awkward01:47
fennso not from the same culture01:47
ebowdenI live in Tasmania.01:47
fennoo the plot thickens01:47
ebowdenWe've a 51% functional literacy rate.01:47
Viper168are you a devil?01:47
fenna tiger?01:48
ebowdenSo we've a lot more religious fanatics.01:48
ebowdenNo.01:48
ebowdenThough some of my relatives are part sheep.01:49
ebowden:D01:49
fennmost rural areas are highly religious, nothing special about tasmania there01:49
Viper168I live in missouri, there are worse places but it's still thick here01:49
Viper168I was raised first baptist then nazarene01:49
Viper168went to catholic school01:49
ebowdenfenn: Tasmania is actually worse than most rural place.01:49
Viper168and then a mormon school01:49
Viper168so I was in trouble a lot01:49
Viper168:P01:50
ebowdenWhy were you in trouble?01:50
ebowdenWere you an Atheist and/or EVILUTIONIST?01:50
ebowden:301:50
ebowdenI want to make a satanic temple school.01:50
Viper168being a pain in the ass by questioning constantly, and not obeying without reason01:50
Viper168never really did anything that bad01:50
Viper168just against the rules, stupid rules01:51
fennthat happens at secular schools too btw01:51
Viper168lol01:51
Viper168they tend to be really strict about authority01:51
fenn"you have no constitutional rights in school" was something we heard every week01:51
Viper168I went to public schools too, was in trouble there too01:51
Viper168but much less often01:52
Viper168the catholic school was especially strict01:52
Viper168damn nuns01:52
jrayhawkfenn: 5-formylcytosine and 5-carboxylcytosine look to be the other eukaryotic ones01:53
Viper168but I did have to spend a couple months in a room by the front offices at the mormon school to do homework I didn't do before01:53
jrayhawkif you find any papers working out what the hell those do, please let me know01:53
Viper168aced tests because they were quick to do and I knew it, just didn;t tolerate busywork01:53
fenni still haven't figured out what the methyl groups do01:53
fennepigenetics came into force after i went to school01:54
ebowdenAt my catholic high school, it's not particularly strict. One of my teachers, an engineer, when some boys were rough-housing in his class, in his typical style of wit he said: "Hey! This is a catholic school, that kind of thing is meant to be between a man and a woman. Or a priest and a boy."01:54
Viper168lol01:54
jrayhawk5mC increases expression, 5hmC decreases expression, as near as I can gather.01:54
fennsomething about unwinding dna and making it avaiable for transcription01:54
fennbut there are plenty of other ways to do that01:55
Viper168mine was more being scolded again for not doing homework when my tests scores were so high01:55
Viper168that pissed them off more than anything01:55
Viper168they wouldn't have been as angry if I were just dumb01:56
Viper168should have faked it01:56
jrayhawkAyup, biology always has more complications up its sleeve, so I am sure there are additional functions and caveats.01:56
ebowdenIQ is inversely correlated with conscientiousness.01:56
fenn" 5-Formylcytosine, an oxidation product of 5-Hydroxymethylcytosine and possible intermediate of an oxidative demethylation pathway"01:56
Viper168the more you know, the more reason you have to be grumpy01:57
Viper168lol01:57
fenn"5-carboxylcytosine (5caC) is the final oxidized derivative of 5-methylcytosine "  so they might just be partially metabolized methyl groups01:57
Viper168I get the impression that higher dopamine levels tend to lead to more impulsive irrational thought, lower being the opposite01:58
Viper168so maybe that has something to do with it01:58
ebowdenNot quite.01:58
ebowdenIt's a balance.01:58
jrayhawkPacBio's real proud of its SMART sequencing machines for being able to sequence all eight, plus piles of other prokaryotic modifications.01:59
ebowdenLow dopamine makes you dumb, as does very high dopamine.01:59
fenn"dumb" is not a very scientific word01:59
ebowdenIt's blunter.01:59
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Viper168at a point a low becomes an obstacle yes02:00
fennViper168: mania and impulsive irrational thought seem to have more to do with GABA and glutamine/glutamate imbalance, resulting in a lack of inhibitory neuron action02:01
ebowdenI wonder what will come of that tiny buckyball study people are currently working to replicate.02:01
fennhigh dopamine can result in psychosis if it's also accompanied by lack of sleep02:02
Viper168ebowden, for very tiny soccer games?02:02
fennViper168: ebowden is talking about the mouse longevity study with C60 + olive oil02:02
ebowdenNo, dissolved c60 buckminsterfullerenes.02:02
Viper168from what I've read it doesn;t even need to include lack of sleep02:02
ebowdenFenn, yup.02:02
ebowdenThe study was not exactly the best in the world.02:03
Viper168excessive l-dopa supplementation can cause is supposedly alone02:03
Viper168*it02:03
Viper168I need some of that NAD+02:03
Viper168I think it was02:03
fennhm. okay. some people take huge doses of l-dopa02:03
ebowdenFenn: I'll be waiting for the replication studies to come out.02:04
Viper168or was it nac02:04
Viper168can't remember02:04
ebowdenNAD+ can be toxic.02:04
Viper168there was one protein that returns a heart to a younger state reducing thickening02:05
ebowdenI think it was another chem that increases levels of NAD+ that was used.02:05
Viper168the one they found that lowered in concentration in againg mice02:05
ebowdenGDF-9?02:05
fennGDF-1102:05
ebowdenAh, that was it.02:05
Viper168but when it was increased with blood from younger mice repaired them02:05
Viper168I beleve so, something like that02:05
fenn"GDF11 has been identified as a blood circulating factor that has the ability to reverse cardiac hypertrophy in mice as a result of hypertrophy related to aging."02:06
ebowdenI wonder what will come of all those people downing NSI-189.02:06
Viper168some of that stuff needs more time, who know what neurological disorders it could cause02:07
ebowdenSome of those people swallow experimental drugs like candy.02:07
Viper168with crazy new classes of drug02:07
Viper168I understand if it's similar enough to something we know02:07
ebowdenIt is promising at least.02:07
Viper168but completely new things, it could cause disorders we haven't even seen yet02:07
ebowdenLOL, late onset autism.02:08
fenni salute our guinea pigs for their courageous and ill-advised sacrifice02:08
ebowdenMe too.02:08
fennthough usually it's just due to bad economic circumstances02:08
fennsame as military really02:08
ebowdenI think combining P7C3A20, a molecule that potently blocks neural cell death with NSI-189, a neurogenesis inducer might get quite a bit of brain growth.02:10
ebowden(By combining, I mean co-administering.)02:10
ebowdenBut, even without anything else with it, NSI-189 will almost certainly have side effects. New, immature neurons disrupt working memory networks.02:12
ebowdenTemporarily.02:12
ebowdenUntil they mature.02:12
jrayhawkre: "so they might just be partially metabolized methyl groups": or just outright damaged by oxidative stress02:12
fennso pacbio finally got a product to market?02:13
jrayhawkbut, like, even then, questions like "does this completely break transcription" are still interesting02:13
ebowdenPacbio?02:13
fennpacificbiosciences.com02:13
ebowdenAh, ok.02:14
ebowdenI'd love to see someone get an unprecedented increase in brain volume from taking a massive combo of neurogenic drugs. It'd be so cool.02:14
fennthey had a too-awesome-to-be-true technology in the lab for far too long02:14
jrayhawkCan't say as I've tried to buy one, but SMRT is advertised as a product and there are lots of papers being published, at least.02:15
ebowdenOh?02:15
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fennis this the same technology as the zeptoliter evanescent waveguide stuff?02:15
jrayhawkdoesn't sound familiar02:16
fenni think it is, and they just renamed it to SMRT to shed the stigma of having a product in development hype mode for so long02:16
fenn"With an active polymerase immobilized at the bottom of each ZMW, nucleotides diffuse into the ZMW chamber. In order to detect incorporation events and identify the base, each of the four nucleotides A, C, G and T are labeled with a different fluorescent dye having a distinct emission spectrum. Since the excitation illumination is directed to the bottom of the ZMW, nucleotides held by the02:17
fennpolymerase prior to incorporation emit an extended signal that identifies the base being incorporated."02:17
fennthey don't actually explain what ZMW stands for (duh) but it's "zero mode waveguide" which is a hole smaller than the excitation wavelength02:17
fennlike the grate on your microwave02:20
jrayhawkhttp://www.youtube.com/user/PacificBiosciences has some fun stuff02:21
jrayhawkhttp://scholar.google.com/scholar?q=smrt+sequencing and lots of papers02:21
fenni eagerly await our methylated overlords02:28
jrayhawkwe are the methylated overlords02:28
jrayhawkwell, those of us without MTHFR problems or crappy diets02:28
* fenn ahem02:29
jrayhawkman, that waveguide stuff is terrifying mad science02:31
fennterrifyingly clever02:31
fennso if their single molecule sequencing works, why don't we have a complete human genome yet?02:32
jrayhawkhttps://twitter.com/DukeSequencing/status/373427511272538112 huh, some details here02:36
fennseems they can read at least 10kb at a time02:36
fenn20k even02:36
jrayhawkhttp://www.nature.com/nbt/journal/v31/n11/full/nbt.2705.html02:37
paperbothttp://libgen.org/scimag/get.php?doi=10.1038%2Fnbt.270502:37
fennthat ought to be long enough to piece together multiple repeat regions02:38
jrayhawkhttp://blog.pacificbiosciences.com/2013/10/resolving-complex-regions-in-human.html02:39
fennhehe http://blog.pacificbiosciences.com/search/label/genome%20finishing02:43
jrayhawkhopefully somebody will release videos from the ASHG conference from a couple weeks ago02:43
fenn(just laughing about the fact that they have a tag for "genome finishing")02:43
jrayhawki only accept grass-finished genomes02:44
fennarabidopsis Genome size: 124.6 Mb02:45
fennSum of Contig Lengths: 124.57 Mb02:45
jrayhawkhttp://blog.pacificbiosciences.com/2014/10/ashg-2014-new-look-at-human-genome-with.html i guess you could see if registering for recordings works02:46
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fenni'm not that into genomics02:48
jrayhawkwell, it sounds from the email they just sent like a useful thing might still happen, so hooray!02:49
jrayhawkjust not immediately02:49
fennit seems like epigenetics would be much more of a hassle for bioinformatics because each base would have a floating point number associated with it, (a ratio, proportional to methylation count/number of reads) making it much harder to set a baseline genome for data compression the way SNP maps work02:54
fennso instead of a 10MB file you have a 10GB file02:54
fennand that genome is different for every cell02:56
fenner.. nevermind about that last bit, each cell would have just a list of epi-SNP's02:57
fennseems like the only way to get a complete epigenome is to throw the whole human into a meat grinder03:02
jrayhawkit's entirely possible that no two nuclei have the same sequence, so, yeah, we'd have to characterize tissue gradients and a lot of stochasticism.03:16
jrayhawktranscriptome stuff i expect will be way cooler in the long run03:18
fennwell not even considering methylation, there are multiple independent somatic gene lines, mosaicism, viral recombination03:18
fennas the embryo grows, individual mutations get propagated to the daughter cells03:18
jrayhawkoh, yeah, that'd be cool to track03:19
fennyou can see some evidence of this with blaschko lines03:19
fenn.wik blaschko lines03:19
yoleaux"Blaschko's lines, also called the Lines of Blaschko, are lines of normal cell development in the skin. These lines invisible under normal conditions. They become apparent when some diseases of the skin or mucosa manifest themselves according to these patterns." — http://en.wikipedia.org/wiki/Blaschko_lines03:19
fennugh nice armpit picture03:20
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fennhttp://scienceblogs.com/pharyngula/2010/08/12/blaschkos-lines/03:21
fennhrm maybe this is just a turing pattern due to growth factor diffusion03:22
jrayhawkhttp://scienceblogs.com/pharyngula/wp-content/blogs.dir/470/files/2012/04/i-83fe4ec386564e5ca9bd0caf2fa69dc9-blas_back.jpeg wicked cool tattoo, bra03:22
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fenn"Women have two X-chromosomes, but men only have one; to maintain parity in the regulation of expression of X-linked genes, women completely shut down one X. Which one is shut down is entirely random." derr what??03:29
fennhow did i not know about this https://en.wikipedia.org/wiki/X-inactivation03:31
archelsthat's what I'm thinking right now03:31
fennhow is an entire chromosome inactivated?03:35
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fenni guess it gets covered with a huge blob of RNA and then methylated to death03:41
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fennhello chido04:32
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chidofenn: hey04:44
fennchido can you make a stain to visualize human X-inactivation?04:49
fenncontext http://scienceblogs.com/pharyngula/2010/08/12/blaschkos-lines/04:51
fennand calico cats04:51
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fennoh well05:06
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chris_99paperbot: http://link.springer.com/chapter/10.1007/11967668_1606:19
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kanzure.title https://www.neuro.mpg.de/borst06:38
kanzure(tungsten electrodes)06:39
yoleauxkanzure: Sorry, that command (.title) took too long to process.06:39
kanzurei guess i can't blame ebowden for being a moron anymore now that i know he's trapped in catholic school06:40
kanzurefly connectome stuff https://www.neuro.mpg.de/30076/borst_p206:42
kanzure.wik serial block-face scanning electron microscopy06:43
yoleaux"Serial block-face scanning electron microscopy (SBEM, SBSEM or SBFSEM) is a method to generate high resolution three-dimensional images from small samples, often biological samples such as brain tissue. A serial block-face scanning electron microscope consists of an ultramicrotome mounted inside the vacuum chamber of a scanning electron  …" — http://en.wikipedia.org/wiki/Serial_block-face_scanning_electron_microscopy06:43
kanzure"EyeWire is a game to map the brain from Sebastian Seung's Lab at MIT. This citizen science human-based computation game challenges players to map 3D neurons in a retina. Eyewire was officially launched on December 10, 2012 and has since grown to over 150,000 players from 140+ countries."06:43
kanzure"Generating 3d models of skin cells using serial block-face scanning electron microscopy" http://ftp.gatan.com/files/PDF/products/app_notes/App_3View_Skin_Cell_Application_Note_FL1.pdf06:44
kanzurepaperbot: http://www.sciencemag.org/content/343/6170/529.short06:46
paperbothttp://libgen.org/scimag/get.php?doi=10.1126%2Fscience.124679406:46
kanzure"Many benthic marine animal populations are established and maintained by free-swimming larvae that recognize cues from surface-bound bacteria to settle and metamorphose. Larvae of the tubeworm Hydroides elegans, an important biofouling agent, require contact with surface-bound bacteria to undergo metamorphosis; however, the mechanisms that underpin this microbially mediated developmental transition have been enigmatic. Here, we show that a ...06:46
kanzure... marine bacterium, Pseudoalteromonas luteoviolacea, produces arrays of phage tail–like structures that trigger metamorphosis of H. elegans. These arrays comprise about 100 contractile structures with outward-facing baseplates, linked by tail fibers and a dynamic hexagonal net. Not only do these arrays suggest a novel form of bacterium-animal interaction, they provide an entry point to understanding how marine biofilms can trigger animal ...06:46
kanzure... development."06:46
kjskjskjsI only learned on Friday that a scanning electron microscope actually only scans a point of the sample at a time06:51
kjskjskjsthus the name06:52
kjskjskjsI somehow had the idea that it bathed the sample in an electron beam and then focused the scattered electrons with a magnetic lens06:52
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kjskjskjsinto an image06:52
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kjskjskjsbut no, it scans the focus point of the electron beam over the sample, measuring the crude quantity of electrons scattered into the detector from each point06:53
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kanzurehm.07:48
FourFirekanzure: are you signed up for cryo, or planning to?07:54
kanzurei'm currently practicing large quantities of cognitive dissonance on that subject08:02
kanzure"pfft i can do it later"08:02
justanotheruserthanks to quantum immortality, I'm living forever08:02
kragenjaviersitaheh08:03
kanzurethanks to cognitive dissonance, you are already dead08:03
justanotheruserpls08:03
kragenjaviersitajustanotheruser: as long as you don't build an Anthropic Principle Machine to collapse the metastable false vacuum, I don't mind you believing that08:04
justanotheruserkragenjaviersita: 5/22 of those words require googling08:05
justanotheruseractually 608:05
yorickwe should strive to do better than that08:06
kragenjaviersitai'm not sure googling will be enough08:07
kragenjaviersitawell, if you believe in the Ridiculously Strong Anthropic Principle, you will experience only the many-worlds branches in which you continue to exist (which I assume is what you mean by "quantum immortality")08:08
kragenjaviersitaif that were true, then an easy way to get what you want would be to destroy the universe whenever something happens that you don't like08:08
kragenjaviersitaentering the lottery and not winning, for example08:09
yorickin a worm fanfic there was a guy with the superpower to see how long people had to live, so he could just commit to killing people at the first sign of trouble in his plans, and then plan until they survived08:10
eudoxiaif you destroy the universe but nobody observes it because they're all dead, can you really say it happened?08:10
justanotheruserHow Can We See If Our Eyes Aren't Even Real?08:11
kragenjaviersitaeudoxia: that is the idea.  unfortunately I think that the more likely outcome of this approach would simply be destroying the universe, that's all08:11
eudoxiaoh, well. plenty of other universes to move to. probably.08:11
kanzureeudoxia: are we absolutely certain that ralph merkle is the same ralph merkle from the cryptology/cryptography world?08:11
FourFirekanzure: I feel the same way, but I'm sure I'll regret it for an instant while getting hit by a bus08:11
kragenjaviersitayorick: that took me a while to understand, but now I do.  interesting08:12
kragenjaviersitakanzure: as sure as one can practically be of a thing08:12
kragenjaviersitabut not absolutely sure08:12
kanzurewhat is the evidence though08:12
eudoxiakanzure: maybe there are like, two twink merkles, and each focused on a different area to get prestige08:12
kanzuredo they look te same?08:12
eudoxiatwin*08:13
FourFirekragenjaviersita: that approach is used in a Peter F. Hamilton book08:13
kanzurei have only ever seen the nanotechnology/cryopreservation ralph merkle08:13
FourFireI'm watching his presentation that you linked the other day now08:13
FourFireon cryo08:14
eudoxiathe singularity university one?08:14
kanzurehttp://www.merkle.com/papers/Thesis1979.pdf08:14
kanzureandytoshi: 608:14
kanzureandytoshi: 608:14
kanzurehmm shift is broken. fuck it.08:14
andytoshi7!08:15
kragenjaviersitakanzure: also http://www.computerhistory.org/fellowawards/hall/bios/Ralph,Merkle/08:15
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kanzure"A good market for cheap reagents or a few good suppliers of cheap reagents+optics would do more for DIY bio than all the kickstarted copycat hardware in the world (with the exception of fluid handling robots maybe)"08:34
kanzurehuh? that market doesn't already exist smewhere?08:34
kanzure*somewhere08:35
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kanzure"test your frontend against a real api" http://reqr.es/ https://news.ycombinator.com/item?id=858207508:42
kanzureheath: ^08:43
kanzure.title https://news.ycombinator.com/item?id=858325708:45
yoleauxFirefox Developer Edition | Hacker News08:45
kanzureParahSailin_: if there's really no website/market for "definitive place to find cheap reagents" then it seems like this should be corrected. or is the problem that there's just honestly no cheap reagents anywhere whatsoever?08:46
kanzurei guess maybe http://store.p212121.com/08:49
kragenjaviersitakanzure: maybe alibaba?08:49
kragenjaviersitacivil liability is a big concern of reagent suppliers in the US08:49
kragenjaviersitawell, I don't actually know that08:49
kanzureyou could sell cheap reagents to labs-only if you cared about that08:50
kanzurealso it doesn't have to be direct sales either08:50
kanzureit can just be a marketplace, search engine, ads/listings, or some stupid blog08:50
kragenjaviersitaI do know that civil liability is a big concern of manufacturers in the US generally; that Armadillo Aerospace had to abandon its hydrogen-peroxide-oxidizer rocket design about ten years ago because they couldn't get suppliers to sell to them;08:50
kanzurewhen john carmack asks for hydrogen-peroxide you better give it to him08:51
kragenjaviersitathat civil liability suits frequently name chemical manufacturers as defendants for damages produced by end-users of their chemicals (I was in the jury pool for a case against a chemical supplier because dry-cleaning shops had disposed of used perchloroethylene improperly in Sacramento);08:52
kanzurethey er... they let you of all people serve on a jury?08:52
kanzurewere they rigging it??08:52
kragenjaviersitaI was in the pool, but I wasn't selected because I told them I was leaving the country befor the trial would end08:52
kanzureah08:53
kragenjaviersitaand I know that many reagent suppliers sell only to labs, and that they refuse to sell even to distributors like Lab-Pro that sell to private citizens;08:53
kragenjaviersitaso from all of this I infer that civil liability is a big concern of reagent suppliers in the US, but I don't have actual knowledge that that's what's going on08:53
kragenjaviersitafor all I know they could be worried about the DEA08:53
kragenjaviersita(which is the reason for a similar problem here in Argentina)08:54
kragenjaviersitaanyway, labs aren't very price-sensitive08:54
kanzurebiotech companies could be, though08:55
kanzureselling to poor customers is a bad idea08:55
kanzurehmm08:55
ParahSailin_really, a real company was not allowed to buy peroxide?08:55
kragenjaviersitayeah08:56
kragenjaviersitapresumably they were worried about peroxide eating somebody's face off and then having to pay damages08:56
kragenjaviersitahttp://armadilloaerospace.com/n.x/Armadillo/Home/News?news_id=296 gives some details08:58
kragenjaviersitahttp://armadilloaerospace.com/n.x/Armadillo/Home/News?news_id=232 talks about their supplier problems in 2003, which were solved at the time, but which you will note the above item clarifies that they returned08:59
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kragenjaviersitaapparently there were only a couple of US suppliers of peroxide for fuel, and one of them (X-L Space Systems) went out of business09:03
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kragenjaviersitathe 2005 item, however, says that the real reason they quit using peroxide wasn't supplier problems, but because they couldn't find a monopropellant peroxide catalyst that would withstand repeated firing cycles09:05
kragenjaviersitaobviously they lost a lot of months of looking for it by not having suppliers, though09:05
kragenjaviersitahttp://armadilloaerospace.com/n.x/armadillo/home/faq however says: "Armadillo would later abandon hydrogen peroxide propellant when supply issues became an unsolvable problem"09:10
archelscyberpunk? https://www.youtube.com/watch?v=GNoOiXkXmYQ09:12
kanzure.title09:14
yoleauxAerial Burton 3D display projects images into mid-air #DigInfo - YouTube09:14
kragenjaviersitaDigInfo looks like a really interesting channel09:17
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nmz787_iis there a language that escapes spaces as #20  ?09:48
rak[1]not that i know of, but i know of a language that doesn't escape spaces at all!10:08
kanzure 10:14
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chris_99i'm not sure i buy this - http://idenux.com/10:22
chris_99"Your heart signal is as unique as your fingerprint. It can be passively and continuously monitored, ensuring it is the same user at any point in time."10:23
nmz787_iI think Intel has a bracelet that does that10:28
chris_99hmm apparently other people are doing it too10:28
chris_99yeah intel seems to have bought some biometric company10:28
chris_99if the heart beat is unique enough, that is cool10:30
nmz787_ihttp://iq.intel.com/new-wearable-sports-jersey-lets-you-see-what-messi-sees/10:30
chris_99haha10:31
nmz787_ihttp://gizmodo.com/what-an-intel-and-fossil-team-up-could-mean-for-smartwa-163159943010:31
nmz787_i'For Intel, this isn't too shocking as this mimics their recent decision to team up with SMS Audio on their upcoming biometric earbud.'10:32
nmz787_i'As we reported earlier, 50 Cent and SMS Audio announced a new partnership with Intel this evening.'10:33
nmz787_ilol10:33
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nmz787_iI never imagined I might meet 50 cent... but now who knows10:33
archelspaperbot: http://iopscience.iop.org/0957-4484/24/47/475301/pdf/0957-4484_24_47_475301.pdf10:45
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kragenjaviersitanmz787_i:  10:52
kanzurenmz787_i: of course you will meet 50 cent11:02
kanzurealso you will become an honorary member of wu tang clan11:04
kanzure(nsh first, though. he's been queued up for a while.)11:05
nsh\o/11:07
kanzurensh: having an actual felony on your record might help your case with them11:11
* nsh nods11:12
nshi've tried to make it as clear as possible that i'm perfectly happy to be convicted in absentia11:12
nshand punished in absentia11:12
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kanzurehrm12:46
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paperwatcherpaperbot: http://www.sciencedirect.com/science/article/pii/S016816561400159X12:57
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/%0A%20Computer-aided%20design%20for%20metabolic%20engineering%0A%20.pdf12:57
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kanzure.title https://news.ycombinator.com/item?id=858343013:05
yoleauxSelf-tightening nut that provides tight fastening with a unique screw thread | Hacker News13:05
kanzure"I'm a former mechanical engineer specializing in fastening (now I'm a Javascript developer)."13:05
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kanzuredamn that's a steep fall13:06
kanzurehttp://jamesgolick.com/2013/5/19/how-tcmalloc-works.html13:06
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delinquentmeyoull liked deze nuts https://www.youtube.com/watch?v=p8LGO68ZPlg13:51
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kanzure.title14:04
yoleauxSelf-tightening nut that provides tight fastening with the aid of a unique screw thread #DigInfo - YouTube14:04
kanzurelegal docz https://swartzfiles.com/14:14
kanzurealthough none of them seem particularly new14:14
ebowdenpaperbot: http://www.ncbi.nlm.nih.gov/pubmed/2407152514:31
paperbothttp://libgen.org/scimag/get.php?doi=10.1016%2Fj.neuroimage.2013.09.03814:31
ebowden\:D/14:32
ebowdenApparently, in cases where there are changes in IQ during early development, those who's cortexes thin have lower IQs, whilst those who's cortexes to do not thin have higher IQs.14:35
ebowdenSo, people who show less cortical thinning in the later stages of development have higher increases in IQ.14:35
ebowdenI wonder if administering a drug that blocks nerve cell death to children deemed to have a higher risk of developing lower IQ might rescue these deficits.14:36
delinquentmeebowden, you're looking at your MRI scans or something?14:36
ebowdenLooking at the paper.14:36
delinquentme"have a higher risk of developing lower IQ"  lelz14:36
ebowdenCognitive ability changes and dynamics of cortical thickness development in healthy children and adolescents.14:36
delinquentmeyeah but Im curious why you're excited about this14:37
delinquentmeor about specifically the thinning ... unless you've got it14:37
delinquentmePS! IF ANYONE WANTS AN MRI .. i've got a friend in SF who needs volunteers14:37
delinquentme7 TSLA MRI14:37
ebowdenheh14:37
delinquentmebig fooker14:37
ebowdenVolunteers for what?14:37
delinquentmebrain scans14:37
ebowdenI guessed that much.14:38
ebowdenWhat experiment is he conducting?14:38
delinquentmeand rebar impailments14:38
delinquentme( fineprint)14:38
delinquentmedidn't ask14:38
delinquentmeand its a she14:38
ebowdenOk.14:38
delinquentmeshes kinda cute14:38
delinquentmebut yeah I wanna maintain that conneciton .. so sending my friends hahah14:38
ebowdenI considered putting he/she, but thought it cumbersome.14:39
delinquentmeagreed14:39
delinquentmeebowden> \:D/14:39
delinquentmescoliosis?14:39
ebowdenThe \:D/ was because paperbot worked and spat out a working link to a delicious paper.14:40
delinquentmetrue but your head is sideways14:41
* delinquentme concerned14:41
ebowdenI find the findings exciting because it means there may be a potential path to treating and preventing an array of cognitive deficits.14:41
ebowdenheh14:41
streetyI hadn't realized until recently that there may be some risks with MRI. I had thought it was safe but expensive14:45
ebowdenOh?14:45
streetyWould be nice to have an imaging modality that permitted safe serial scans over a lifetime14:45
streetyapparently some risk of DNA breaks14:46
delinquentmeissues associated with snapping every orbit of every electron in your body on and off ?14:46
delinquentmeI mean any folding / binding in your body happening within that time ... will be influenced ... no?14:46
streetywell when you put it like that . . .14:47
delinquentmeto a greater or less extending depending on the local attraction strength of the bonds14:47
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delinquentmeits fucking nuts that we can do that14:47
streetyIt would be even better if it was something I could pull off in my garage14:53
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delinquentmedoes your garage have a concrete bed?15:00
delinquentmeMRI = a few tons right?15:00
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nmz787_idelinquentme: do you think a web-app that gave a person control of a FIB or SEM would make $$$?15:06
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kanzureperhaps as a gimmick15:06
nmz787_idelinquentme: they wouldn't be able to put their own sample in, but could do some kind of flavor-of-the-week (or evening)15:06
nmz787_itour around some old IC15:06
nmz787_iwould have to be like $5 or $6 per minute15:07
nmz787_ibut I imagine there are a handful of people with that money and level of interest15:07
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streetyBuilding a sufficiently strong base for the MRI would seem like a fairly small issue when compared to building the MRI itself (or other imaging system)15:09
ebowdenI wonder, if we had drugs that extended childhood brain development and resulted in appreciable increases in IQ, how much might parents pay for them...15:12
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kanzure"wysiwyg editor for network packets" https://wireedit.com/ ("WireEdit is a packet editor, not the analyzer. No real-time packet capture either.")15:30
kanzurehttps://news.ycombinator.com/item?id=858471915:30
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delinquentmenmz787, its cool from a concept standpoint ... but like is this a perfectly functional FIB?15:56
delinquentmeadjustments / alignments could be a pain in the ass15:56
delinquentmeyou gotta find the use case15:56
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delinquentmestreety, IDK if I'd build an MRI ... but I suppose you could ...16:00
delinquentmehttps://www.youtube.com/watch?v=zksVZCJajCI16:01
streetywas that link for me? https://www.youtube.com/watch?v=hF3V-GHiJ78 seems more relevant16:05
delinquentmehaha streety so you know of him !16:07
streetyone of those people I repeatedly rediscover16:08
streetycertainly worked on some interesting projects16:09
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delinquentmeso fucking nuts. https://www.facebook.com/video.php?v=75445298460952816:20
delinquentmeim sweating.16:23
kanzure.title16:24
yoleauxhookgrip | Facebook16:24
nmz787_idelinquentme: yep, fully functional FIB... I would have to limit what the user could do to some extent, to prevent physical damage... that would be more work than something as simple/stupid as just opening up VNC to the FIB machine... but I'm already doing screen captures of the machine's live-image window16:37
nmz787_iand working on an arduino-controlled mouse for the machine16:38
nmz787_iso users would at least be able to move around the sample, zoom, focus, etc... I'm going to add an autofocus algorithm too, so that would be available to newbs16:39
delinquentmehttps://www.youtube.com/watch?v=ZQUTJjWvx3I16:43
delinquentmesome of my fav16:43
delinquentmenmz787, do you know andrew zoneneberg?16:43
delinquentmehes building out something sim lar16:43
delinquentme" yell racial slurs from a moving vehicle " ... " then get out "16:44
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delinquentmeOHHHHHHH BTW.17:49
delinquentmeinterviewed with a CTO for a company around here ... asked him what were his experiences / practices around rebasing17:50
delinquentmewas clueless.17:50
caternis rebasing a biology thing or are you talking about git17:50
delinquentmeya . git17:50
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delinquentmeERMERGER18:23
delinquentmerunning.18:23
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nmz787_pdelinquentme: I internet-know him19:18
nmz787_pI don't know of him modifying FIBs though, using them sure19:18
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delinquentmeheheheh nmz787 i internet-know 90% of my friends21:46
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delinquentmegeeeeze. so good https://www.youtube.com/watch?v=UwdLUuAjM9M&list=PLcghjaDFUHglje0wiMUDMTrUV6z5wGGQq&index=3522:41
delinquentmefunk + dance electro ... with the occasional almost scream?? https://www.youtube.com/watch?v=oA9cmPG_a8I&index=39&list=PLcghjaDFUHglje0wiMUDMTrUV6z5wGGQq ... really good .. really weird.22:57
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fennthat DIY CT/x-ray scanner seems really useful for automated reverse engineering23:10
fennmuch better results than most laser scanners23:11
fennand you can probably do texture scanning at the same time, if you're into that sort of thing23:11
fennlots of noise though; i think his x-ray beam was not strong enough23:12
fennmultiple exposure levels per angle would give you a higher dynamic range for things with both metal and organic materials23:13
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fennyou can get near arbitrary resolution by having a larger screen and zooming in23:24
fenni saw a 3d reconstruction of a tick with synchrotron light, down to cellular resolution23:25
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fennomg CT images are so cool23:29
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fenn.title http://www.nature.com/nature/journal/v442/n7103/fig_tab/nature04890_F1.html23:37
yoleauxFigure 1 : Synchrotron X-ray tomographic microscopy of fossil embryos : Nature23:37
fennyou might be able to read books without opening them, if they used iron based pigments23:41
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--- Log closed Tue Nov 11 00:00:47 2014

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