--- Log opened Mon Nov 10 00:00:46 2014 | ||
jrayhawk | this 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 |
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jrayhawk | though for humans that's s/mutants/epimutants/ | 00:02 |
fenn | i'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 humans | 00:08 |
fenn | we can revise the research later once we figure out how to get people in "non pathological" situations | 00:09 |
fenn | there 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 heroin | 00:11 |
fenn | ...in "the real world" | 00:12 |
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fenn | in 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 been | 00:23 |
fenn | administered 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 |
jrayhawk | people working from sane null hypothesis jump ahead of the science by decades | 00:26 |
jrayhawk | hypotheses | 00:27 |
jrayhawk | e.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 |
fenn | but weston price had to trek all over the world just to find the mythical humans living in utopia | 00:38 |
jrayhawk | Ayup, he worked hard to find the highest quality null hypothesis available to him. | 00:40 |
jrayhawk | And it's a crying shame more people didn't steal his fine work. | 00:40 |
fenn | he was a bit out of his field... nutrition/biochem vs dentistry | 00:41 |
jrayhawk | Anthropology is even further out. | 00:41 |
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jrayhawk | It's nice that universities are getting EvoS programs for this sort of thing. | 00:43 |
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fenn | what does EvoS stand for? | 00:48 |
jrayhawk | Evolutionary Studies; a departmental cross-pollination effort. | 00:49 |
jrayhawk | "multidisciplinary" i guess is the usual term | 00:49 |
fenn | so uh, can we assume that biology is a discipline which already takes evolution into account? | 00:51 |
jrayhawk | Not usually. | 00:51 |
fenn | then i don't know what the hell you're talking about | 00:51 |
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fenn | evolution.binghamton.edu/evos/ also does a really bad job of explaining itself | 00:52 |
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 |
fenn | hah good luck with that | 01:00 |
jrayhawk | even now it's very hard for researchers to discuss group selectionism | 01:01 |
fenn | because group selection has been proven not to exist? | 01:01 |
fenn | (is "group selectionism" the same thing as "group selection"?) | 01:02 |
jrayhawk | no, there's just immense political pressure to pretend so. | 01:02 |
jrayhawk | http://www.christopherxjjensen.com/2010/10/13/robert-trivers-and-colleagues-on-nowak-tarnita-and-wilsons-the-evolution-of-eusociality/ | 01:02 |
jrayhawk | sortof how like lamarckianism was disproven right up until it wasn't | 01:03 |
fenn | hmm.. kin selection is one of those philosophical "identity" questions that will never be resolved | 01:03 |
fenn | oh jeez now you're saying lamarckian evolution is true? | 01:04 |
fenn | because of epimutations or something? | 01:04 |
jrayhawk | explain to me how "epigenetics" is different from "lamarckian evolution" | 01:05 |
fenn | lamarckian evolution is theoretically responsible for speciation, and epigenetics is not | 01:05 |
jrayhawk | how would you test that | 01:05 |
jrayhawk | actually that's just a stupid line of questioning; speciation is really poorly defined | 01:06 |
fenn | put a species in difficult situation and see if the adapted ones become a new species and the unadapted ones stay the same species | 01:07 |
fenn | bleh i'm no evolutionary theorist | 01:07 |
* fenn reads on lamarckism | 01:08 | |
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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 balloon | 01:13 | |
fenn | The 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 - to | 01:13 |
fenn | a central focus it never had for Lamarck himself." | 01:14 |
fenn | Examples of what is traditionally called "Lamarckism" would include: | 01:15 |
fenn | Giraffes stretching their necks to reach leaves high in trees (especially Acacias), strengthen and gradually lengthen their necks. These giraffes have offspring with slightly longer necks | 01:15 |
fenn | are you seriously equating this with epigenetics? | 01:15 |
Viper168 | it's more a mutation happens that ends up giving some a longer neck, and those reproduce better | 01:17 |
Viper168 | the mutation happens irrelevant of need, if it gets spread though depends on the situation | 01:18 |
Viper168 | depending on of it's helpful or harmful | 01:18 |
Viper168 | epigenetic changes can be influenced by the environment though | 01:19 |
Viper168 | like the layer that controls how and if genes are expressed | 01:19 |
fenn | Viper168: that is neo-darwinism, not what we are talking about atm | 01:19 |
fenn | jrayhawk: 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 |
Viper168 | I've seen no evidence genes can be directly altered by the environment | 01:23 |
jrayhawk | hahaha | 01:23 |
fenn | but what they really meant is "there's a big old guy on a cloud who thought real hard and magically *poof* life" | 01:25 |
jrayhawk | welp, have fun interpreting everything in the least charitable way possible | 01:26 |
fenn | and the lamarckians really meant that the fat man had fat kids | 01:26 |
fenn | sorry was i wrong about how creationists see things? | 01:26 |
jrayhawk | christ, it's like i am being dragged back into a discussion with nmz | 01:27 |
jrayhawk | Viper168: 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-cytosine | 01:29 |
jrayhawk | there'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 anyway | 01:30 |
jrayhawk | s/eight/at least eight/ | 01:30 |
fenn | acetyl-? | 01:30 |
Viper168 | it seems you're thinking of the wrong person | 01:31 |
jrayhawk | no | 01:31 |
Viper168 | because we have only rarely talked | 01:31 |
Viper168 | and certainly not that often about genetics | 01:31 |
jrayhawk | i think the fact that i am willing to try to talk to you is the only reason kanzure hasn't banned you | 01:32 |
jrayhawk | his motivations are hard to follow, though | 01:32 |
fenn | i was thinking of histone acetylation, nevermind | 01:34 |
Viper168 | you're tripping | 01:34 |
Viper168 | what have you been smoking | 01:35 |
ebowden | Wait, did someone here think Lamarckism and epigenetics are the same thing? | 01:36 |
Viper168 | no | 01:37 |
jrayhawk | yes | 01:37 |
fenn | i see you guys talking about fats and roid rage, but nothing ban-worthy | 01:37 |
fenn | (in the logs) | 01:37 |
Viper168 | someone mistakenly thought someone did | 01:37 |
ebowden | I remember when I saw a creationist I knew of log into the biology channel and I was like "nooooooooooooooooooO!". | 01:39 |
Viper168 | it's worse when you knew them before they went insane | 01:40 |
ebowden | LOL | 01:40 |
Viper168 | when someone just decides to adopt it | 01:40 |
ebowden | Damn. | 01:40 |
Viper168 | just had an old friend do that, it's weird | 01:40 |
Viper168 | now all of his posts online are about jesus | 01:40 |
ebowden | Is that old friend a scientist? | 01:40 |
ebowden | LOL | 01:40 |
Viper168 | if he were much of a scientist, he'd not be making wild assumptions | 01:41 |
Viper168 | but no | 01:41 |
Viper168 | he worked on/stole cars in his past | 01:41 |
ebowden | LOL | 01:41 |
ebowden | Sounds about right. | 01:41 |
ebowden | Did this guy give you creationist propaganda for your birthday? | 01:42 |
Viper168 | it was only in the last few weeks that he went crazy with it | 01:42 |
ebowden | Ah. | 01:43 |
ebowden | Woah. | 01:43 |
ebowden | I've been trying to find someone else who has someone that gives them creationist propaganda for their birthday. | 01:44 |
Viper168 | lol | 01:44 |
ebowden | It seems only me and my brother have that problem. | 01:44 |
Viper168 | there are these people that try to pass it out on weekends here at a popular intersection | 01:44 |
Viper168 | in such instances, I accept satanism as temporarily acceptable to promote | 01:45 |
fenn | ebowden: 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 |
Viper168 | give them a hail satan as I drive by | 01:45 |
Viper168 | I thought about pretending to be with them and help, but have my own pamphlets printed out with something crazy | 01:46 |
Viper168 | and pass those out instead | 01:46 |
ebowden | Viper168: Imagine those people, but they're your brother-in-law, and the pamphlets are supposed to be your birthday presents. | 01:46 |
Viper168 | by crazy, i mean crazy in a way that isn;t familiar to people | 01:46 |
ebowden | fenn: Brother in law. | 01:46 |
ebowden | Not my twin brother. | 01:47 |
ebowden | Just my creepy brother-in-law. | 01:47 |
Viper168 | lol, that would be nice and awkward | 01:47 |
fenn | so not from the same culture | 01:47 |
ebowden | I live in Tasmania. | 01:47 |
fenn | oo the plot thickens | 01:47 |
ebowden | We've a 51% functional literacy rate. | 01:47 |
Viper168 | are you a devil? | 01:47 |
fenn | a tiger? | 01:48 |
ebowden | So we've a lot more religious fanatics. | 01:48 |
ebowden | No. | 01:48 |
ebowden | Though some of my relatives are part sheep. | 01:49 |
ebowden | :D | 01:49 |
fenn | most rural areas are highly religious, nothing special about tasmania there | 01:49 |
Viper168 | I live in missouri, there are worse places but it's still thick here | 01:49 |
Viper168 | I was raised first baptist then nazarene | 01:49 |
Viper168 | went to catholic school | 01:49 |
ebowden | fenn: Tasmania is actually worse than most rural place. | 01:49 |
Viper168 | and then a mormon school | 01:49 |
Viper168 | so I was in trouble a lot | 01:49 |
Viper168 | :P | 01:50 |
ebowden | Why were you in trouble? | 01:50 |
ebowden | Were you an Atheist and/or EVILUTIONIST? | 01:50 |
ebowden | :3 | 01:50 |
ebowden | I want to make a satanic temple school. | 01:50 |
Viper168 | being a pain in the ass by questioning constantly, and not obeying without reason | 01:50 |
Viper168 | never really did anything that bad | 01:50 |
Viper168 | just against the rules, stupid rules | 01:51 |
fenn | that happens at secular schools too btw | 01:51 |
Viper168 | lol | 01:51 |
Viper168 | they tend to be really strict about authority | 01:51 |
fenn | "you have no constitutional rights in school" was something we heard every week | 01:51 |
Viper168 | I went to public schools too, was in trouble there too | 01:51 |
Viper168 | but much less often | 01:52 |
Viper168 | the catholic school was especially strict | 01:52 |
Viper168 | damn nuns | 01:52 |
jrayhawk | fenn: 5-formylcytosine and 5-carboxylcytosine look to be the other eukaryotic ones | 01:53 |
Viper168 | but 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 before | 01:53 |
jrayhawk | if you find any papers working out what the hell those do, please let me know | 01:53 |
Viper168 | aced tests because they were quick to do and I knew it, just didn;t tolerate busywork | 01:53 |
fenn | i still haven't figured out what the methyl groups do | 01:53 |
fenn | epigenetics came into force after i went to school | 01:54 |
ebowden | At 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 |
Viper168 | lol | 01:54 |
jrayhawk | 5mC increases expression, 5hmC decreases expression, as near as I can gather. | 01:54 |
fenn | something about unwinding dna and making it avaiable for transcription | 01:54 |
fenn | but there are plenty of other ways to do that | 01:55 |
Viper168 | mine was more being scolded again for not doing homework when my tests scores were so high | 01:55 |
Viper168 | that pissed them off more than anything | 01:55 |
Viper168 | they wouldn't have been as angry if I were just dumb | 01:56 |
Viper168 | should have faked it | 01:56 |
jrayhawk | Ayup, biology always has more complications up its sleeve, so I am sure there are additional functions and caveats. | 01:56 |
ebowden | IQ 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 |
Viper168 | the more you know, the more reason you have to be grumpy | 01:57 |
Viper168 | lol | 01:57 |
fenn | "5-carboxylcytosine (5caC) is the final oxidized derivative of 5-methylcytosine " so they might just be partially metabolized methyl groups | 01:57 |
Viper168 | I get the impression that higher dopamine levels tend to lead to more impulsive irrational thought, lower being the opposite | 01:58 |
Viper168 | so maybe that has something to do with it | 01:58 |
ebowden | Not quite. | 01:58 |
ebowden | It's a balance. | 01:58 |
jrayhawk | PacBio's real proud of its SMART sequencing machines for being able to sequence all eight, plus piles of other prokaryotic modifications. | 01:59 |
ebowden | Low dopamine makes you dumb, as does very high dopamine. | 01:59 |
fenn | "dumb" is not a very scientific word | 01:59 |
ebowden | It's blunter. | 01:59 |
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Viper168 | at a point a low becomes an obstacle yes | 02:00 |
fenn | Viper168: mania and impulsive irrational thought seem to have more to do with GABA and glutamine/glutamate imbalance, resulting in a lack of inhibitory neuron action | 02:01 |
ebowden | I wonder what will come of that tiny buckyball study people are currently working to replicate. | 02:01 |
fenn | high dopamine can result in psychosis if it's also accompanied by lack of sleep | 02:02 |
Viper168 | ebowden, for very tiny soccer games? | 02:02 |
fenn | Viper168: ebowden is talking about the mouse longevity study with C60 + olive oil | 02:02 |
ebowden | No, dissolved c60 buckminsterfullerenes. | 02:02 |
Viper168 | from what I've read it doesn;t even need to include lack of sleep | 02:02 |
ebowden | Fenn, yup. | 02:02 |
ebowden | The study was not exactly the best in the world. | 02:03 |
Viper168 | excessive l-dopa supplementation can cause is supposedly alone | 02:03 |
Viper168 | *it | 02:03 |
Viper168 | I need some of that NAD+ | 02:03 |
Viper168 | I think it was | 02:03 |
fenn | hm. okay. some people take huge doses of l-dopa | 02:03 |
ebowden | Fenn: I'll be waiting for the replication studies to come out. | 02:04 |
Viper168 | or was it nac | 02:04 |
Viper168 | can't remember | 02:04 |
ebowden | NAD+ can be toxic. | 02:04 |
Viper168 | there was one protein that returns a heart to a younger state reducing thickening | 02:05 |
ebowden | I think it was another chem that increases levels of NAD+ that was used. | 02:05 |
Viper168 | the one they found that lowered in concentration in againg mice | 02:05 |
ebowden | GDF-9? | 02:05 |
fenn | GDF-11 | 02:05 |
ebowden | Ah, that was it. | 02:05 |
Viper168 | but when it was increased with blood from younger mice repaired them | 02:05 |
Viper168 | I beleve so, something like that | 02:05 |
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 |
ebowden | I wonder what will come of all those people downing NSI-189. | 02:06 |
Viper168 | some of that stuff needs more time, who know what neurological disorders it could cause | 02:07 |
ebowden | Some of those people swallow experimental drugs like candy. | 02:07 |
Viper168 | with crazy new classes of drug | 02:07 |
Viper168 | I understand if it's similar enough to something we know | 02:07 |
ebowden | It is promising at least. | 02:07 |
Viper168 | but completely new things, it could cause disorders we haven't even seen yet | 02:07 |
ebowden | LOL, late onset autism. | 02:08 |
fenn | i salute our guinea pigs for their courageous and ill-advised sacrifice | 02:08 |
ebowden | Me too. | 02:08 |
fenn | though usually it's just due to bad economic circumstances | 02:08 |
fenn | same as military really | 02:08 |
ebowden | I 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 |
ebowden | But, even without anything else with it, NSI-189 will almost certainly have side effects. New, immature neurons disrupt working memory networks. | 02:12 |
ebowden | Temporarily. | 02:12 |
ebowden | Until they mature. | 02:12 |
jrayhawk | re: "so they might just be partially metabolized methyl groups": or just outright damaged by oxidative stress | 02:12 |
fenn | so pacbio finally got a product to market? | 02:13 |
jrayhawk | but, like, even then, questions like "does this completely break transcription" are still interesting | 02:13 |
ebowden | Pacbio? | 02:13 |
fenn | pacificbiosciences.com | 02:13 |
ebowden | Ah, ok. | 02:14 |
ebowden | I'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 |
fenn | they had a too-awesome-to-be-true technology in the lab for far too long | 02:14 |
jrayhawk | Can'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 |
ebowden | Oh? | 02:15 |
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fenn | is this the same technology as the zeptoliter evanescent waveguide stuff? | 02:15 |
jrayhawk | doesn't sound familiar | 02:16 |
fenn | i think it is, and they just renamed it to SMRT to shed the stigma of having a product in development hype mode for so long | 02:16 |
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 the | 02:17 |
fenn | polymerase prior to incorporation emit an extended signal that identifies the base being incorporated." | 02:17 |
fenn | they don't actually explain what ZMW stands for (duh) but it's "zero mode waveguide" which is a hole smaller than the excitation wavelength | 02:17 |
fenn | like the grate on your microwave | 02:20 |
jrayhawk | http://www.youtube.com/user/PacificBiosciences has some fun stuff | 02:21 |
jrayhawk | http://scholar.google.com/scholar?q=smrt+sequencing and lots of papers | 02:21 |
fenn | i eagerly await our methylated overlords | 02:28 |
jrayhawk | we are the methylated overlords | 02:28 |
jrayhawk | well, those of us without MTHFR problems or crappy diets | 02:28 |
* fenn ahem | 02:29 | |
jrayhawk | man, that waveguide stuff is terrifying mad science | 02:31 |
fenn | terrifyingly clever | 02:31 |
fenn | so if their single molecule sequencing works, why don't we have a complete human genome yet? | 02:32 |
jrayhawk | https://twitter.com/DukeSequencing/status/373427511272538112 huh, some details here | 02:36 |
fenn | seems they can read at least 10kb at a time | 02:36 |
fenn | 20k even | 02:36 |
jrayhawk | http://www.nature.com/nbt/journal/v31/n11/full/nbt.2705.html | 02:37 |
paperbot | http://libgen.org/scimag/get.php?doi=10.1038%2Fnbt.2705 | 02:37 |
fenn | that ought to be long enough to piece together multiple repeat regions | 02:38 |
jrayhawk | http://blog.pacificbiosciences.com/2013/10/resolving-complex-regions-in-human.html | 02:39 |
fenn | hehe http://blog.pacificbiosciences.com/search/label/genome%20finishing | 02:43 |
jrayhawk | hopefully somebody will release videos from the ASHG conference from a couple weeks ago | 02:43 |
fenn | (just laughing about the fact that they have a tag for "genome finishing") | 02:43 |
jrayhawk | i only accept grass-finished genomes | 02:44 |
fenn | arabidopsis Genome size: 124.6 Mb | 02:45 |
fenn | Sum of Contig Lengths: 124.57 Mb | 02:45 |
jrayhawk | http://blog.pacificbiosciences.com/2014/10/ashg-2014-new-look-at-human-genome-with.html i guess you could see if registering for recordings works | 02:46 |
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fenn | i'm not that into genomics | 02:48 |
jrayhawk | well, it sounds from the email they just sent like a useful thing might still happen, so hooray! | 02:49 |
jrayhawk | just not immediately | 02:49 |
fenn | it 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 work | 02:54 |
fenn | so instead of a 10MB file you have a 10GB file | 02:54 |
fenn | and that genome is different for every cell | 02:56 |
fenn | er.. nevermind about that last bit, each cell would have just a list of epi-SNP's | 02:57 |
fenn | seems like the only way to get a complete epigenome is to throw the whole human into a meat grinder | 03:02 |
jrayhawk | it'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 |
jrayhawk | transcriptome stuff i expect will be way cooler in the long run | 03:18 |
fenn | well not even considering methylation, there are multiple independent somatic gene lines, mosaicism, viral recombination | 03:18 |
fenn | as the embryo grows, individual mutations get propagated to the daughter cells | 03:18 |
jrayhawk | oh, yeah, that'd be cool to track | 03:19 |
fenn | you can see some evidence of this with blaschko lines | 03:19 |
fenn | .wik blaschko lines | 03:19 |
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_lines | 03:19 |
fenn | ugh nice armpit picture | 03:20 |
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fenn | http://scienceblogs.com/pharyngula/2010/08/12/blaschkos-lines/ | 03:21 |
fenn | hrm maybe this is just a turing pattern due to growth factor diffusion | 03:22 |
jrayhawk | http://scienceblogs.com/pharyngula/wp-content/blogs.dir/470/files/2012/04/i-83fe4ec386564e5ca9bd0caf2fa69dc9-blas_back.jpeg wicked cool tattoo, bra | 03:22 |
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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 |
fenn | how did i not know about this https://en.wikipedia.org/wiki/X-inactivation | 03:31 |
archels | that's what I'm thinking right now | 03:31 |
fenn | how is an entire chromosome inactivated? | 03:35 |
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fenn | i guess it gets covered with a huge blob of RNA and then methylated to death | 03:41 |
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fenn | hello chido | 04:32 |
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chido | fenn: hey | 04:44 |
fenn | chido can you make a stain to visualize human X-inactivation? | 04:49 |
fenn | context http://scienceblogs.com/pharyngula/2010/08/12/blaschkos-lines/ | 04:51 |
fenn | and calico cats | 04:51 |
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fenn | oh well | 05:06 |
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chris_99 | paperbot: http://link.springer.com/chapter/10.1007/11967668_16 | 06:19 |
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kanzure | .title https://www.neuro.mpg.de/borst | 06:38 |
kanzure | (tungsten electrodes) | 06:39 |
yoleaux | kanzure: Sorry, that command (.title) took too long to process. | 06:39 |
kanzure | i guess i can't blame ebowden for being a moron anymore now that i know he's trapped in catholic school | 06:40 |
kanzure | fly connectome stuff https://www.neuro.mpg.de/30076/borst_p2 | 06:42 |
kanzure | .wik serial block-face scanning electron microscopy | 06:43 |
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_microscopy | 06:43 |
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.pdf | 06:44 |
kanzure | paperbot: http://www.sciencemag.org/content/343/6170/529.short | 06:46 |
paperbot | http://libgen.org/scimag/get.php?doi=10.1126%2Fscience.1246794 | 06:46 |
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 |
kjskjskjs | I only learned on Friday that a scanning electron microscope actually only scans a point of the sample at a time | 06:51 |
kjskjskjs | thus the name | 06:52 |
kjskjskjs | I somehow had the idea that it bathed the sample in an electron beam and then focused the scattered electrons with a magnetic lens | 06:52 |
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kjskjskjs | into an image | 06:52 |
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kjskjskjs | but 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 point | 06:53 |
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kanzure | hm. | 07:48 |
FourFire | kanzure: are you signed up for cryo, or planning to? | 07:54 |
kanzure | i'm currently practicing large quantities of cognitive dissonance on that subject | 08:02 |
kanzure | "pfft i can do it later" | 08:02 |
justanotheruser | thanks to quantum immortality, I'm living forever | 08:02 |
kragenjaviersita | heh | 08:03 |
kanzure | thanks to cognitive dissonance, you are already dead | 08:03 |
justanotheruser | pls | 08:03 |
kragenjaviersita | justanotheruser: as long as you don't build an Anthropic Principle Machine to collapse the metastable false vacuum, I don't mind you believing that | 08:04 |
justanotheruser | kragenjaviersita: 5/22 of those words require googling | 08:05 |
justanotheruser | actually 6 | 08:05 |
yorick | we should strive to do better than that | 08:06 |
kragenjaviersita | i'm not sure googling will be enough | 08:07 |
kragenjaviersita | well, 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 |
kragenjaviersita | if 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 like | 08:08 |
kragenjaviersita | entering the lottery and not winning, for example | 08:09 |
yorick | in 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 survived | 08:10 |
eudoxia | if you destroy the universe but nobody observes it because they're all dead, can you really say it happened? | 08:10 |
justanotheruser | How Can We See If Our Eyes Aren't Even Real? | 08:11 |
kragenjaviersita | eudoxia: that is the idea. unfortunately I think that the more likely outcome of this approach would simply be destroying the universe, that's all | 08:11 |
eudoxia | oh, well. plenty of other universes to move to. probably. | 08:11 |
kanzure | eudoxia: are we absolutely certain that ralph merkle is the same ralph merkle from the cryptology/cryptography world? | 08:11 |
FourFire | kanzure: I feel the same way, but I'm sure I'll regret it for an instant while getting hit by a bus | 08:11 |
kragenjaviersita | yorick: that took me a while to understand, but now I do. interesting | 08:12 |
kragenjaviersita | kanzure: as sure as one can practically be of a thing | 08:12 |
kragenjaviersita | but not absolutely sure | 08:12 |
kanzure | what is the evidence though | 08:12 |
eudoxia | kanzure: maybe there are like, two twink merkles, and each focused on a different area to get prestige | 08:12 |
kanzure | do they look te same? | 08:12 |
eudoxia | twin* | 08:13 |
FourFire | kragenjaviersita: that approach is used in a Peter F. Hamilton book | 08:13 |
kanzure | i have only ever seen the nanotechnology/cryopreservation ralph merkle | 08:13 |
FourFire | I'm watching his presentation that you linked the other day now | 08:13 |
FourFire | on cryo | 08:14 |
eudoxia | the singularity university one? | 08:14 |
kanzure | http://www.merkle.com/papers/Thesis1979.pdf | 08:14 |
kanzure | andytoshi: 6 | 08:14 |
kanzure | andytoshi: 6 | 08:14 |
kanzure | hmm shift is broken. fuck it. | 08:14 |
andytoshi | 7! | 08:15 |
kragenjaviersita | kanzure: 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 |
kanzure | huh? that market doesn't already exist smewhere? | 08:34 |
kanzure | *somewhere | 08:35 |
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kanzure | "test your frontend against a real api" http://reqr.es/ https://news.ycombinator.com/item?id=8582075 | 08:42 |
kanzure | heath: ^ | 08:43 |
kanzure | .title https://news.ycombinator.com/item?id=8583257 | 08:45 |
yoleaux | Firefox Developer Edition | Hacker News | 08:45 |
kanzure | ParahSailin_: 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 |
kanzure | i guess maybe http://store.p212121.com/ | 08:49 |
kragenjaviersita | kanzure: maybe alibaba? | 08:49 |
kragenjaviersita | civil liability is a big concern of reagent suppliers in the US | 08:49 |
kragenjaviersita | well, I don't actually know that | 08:49 |
kanzure | you could sell cheap reagents to labs-only if you cared about that | 08:50 |
kanzure | also it doesn't have to be direct sales either | 08:50 |
kanzure | it can just be a marketplace, search engine, ads/listings, or some stupid blog | 08:50 |
kragenjaviersita | I 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 |
kanzure | when john carmack asks for hydrogen-peroxide you better give it to him | 08:51 |
kragenjaviersita | that 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 |
kanzure | they er... they let you of all people serve on a jury? | 08:52 |
kanzure | were they rigging it?? | 08:52 |
kragenjaviersita | I was in the pool, but I wasn't selected because I told them I was leaving the country befor the trial would end | 08:52 |
kanzure | ah | 08:53 |
kragenjaviersita | and 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 |
kragenjaviersita | so 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 on | 08:53 |
kragenjaviersita | for all I know they could be worried about the DEA | 08:53 |
kragenjaviersita | (which is the reason for a similar problem here in Argentina) | 08:54 |
kragenjaviersita | anyway, labs aren't very price-sensitive | 08:54 |
kanzure | biotech companies could be, though | 08:55 |
kanzure | selling to poor customers is a bad idea | 08:55 |
kanzure | hmm | 08:55 |
ParahSailin_ | really, a real company was not allowed to buy peroxide? | 08:55 |
kragenjaviersita | yeah | 08:56 |
kragenjaviersita | presumably they were worried about peroxide eating somebody's face off and then having to pay damages | 08:56 |
kragenjaviersita | http://armadilloaerospace.com/n.x/Armadillo/Home/News?news_id=296 gives some details | 08:58 |
kragenjaviersita | http://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 returned | 08:59 |
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kragenjaviersita | apparently there were only a couple of US suppliers of peroxide for fuel, and one of them (X-L Space Systems) went out of business | 09:03 |
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kragenjaviersita | the 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 cycles | 09:05 |
kragenjaviersita | obviously they lost a lot of months of looking for it by not having suppliers, though | 09:05 |
kragenjaviersita | http://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 |
archels | cyberpunk? https://www.youtube.com/watch?v=GNoOiXkXmYQ | 09:12 |
kanzure | .title | 09:14 |
yoleaux | Aerial Burton 3D display projects images into mid-air #DigInfo - YouTube | 09:14 |
kragenjaviersita | DigInfo looks like a really interesting channel | 09:17 |
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nmz787_i | is 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_99 | i'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_i | I think Intel has a bracelet that does that | 10:28 |
chris_99 | hmm apparently other people are doing it too | 10:28 |
chris_99 | yeah intel seems to have bought some biometric company | 10:28 |
chris_99 | if the heart beat is unique enough, that is cool | 10:30 |
nmz787_i | http://iq.intel.com/new-wearable-sports-jersey-lets-you-see-what-messi-sees/ | 10:30 |
chris_99 | haha | 10:31 |
nmz787_i | http://gizmodo.com/what-an-intel-and-fossil-team-up-could-mean-for-smartwa-1631599430 | 10:31 |
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_i | lol | 10:33 |
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nmz787_i | I never imagined I might meet 50 cent... but now who knows | 10:33 |
archels | paperbot: http://iopscience.iop.org/0957-4484/24/47/475301/pdf/0957-4484_24_47_475301.pdf | 10:45 |
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kragenjaviersita | nmz787_i:   | 10:52 |
kanzure | nmz787_i: of course you will meet 50 cent | 11:02 |
kanzure | also you will become an honorary member of wu tang clan | 11:04 |
kanzure | (nsh first, though. he's been queued up for a while.) | 11:05 |
nsh | \o/ | 11:07 |
kanzure | nsh: having an actual felony on your record might help your case with them | 11:11 |
* nsh nods | 11:12 | |
nsh | i've tried to make it as clear as possible that i'm perfectly happy to be convicted in absentia | 11:12 |
nsh | and punished in absentia | 11:12 |
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kanzure | hrm | 12:46 |
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paperwatcher | paperbot: http://www.sciencedirect.com/science/article/pii/S016816561400159X | 12:57 |
paperbot | http://diyhpl.us/~bryan/papers2/paperbot/%0A%20Computer-aided%20design%20for%20metabolic%20engineering%0A%20.pdf | 12:57 |
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kanzure | .title https://news.ycombinator.com/item?id=8583430 | 13:05 |
yoleaux | Self-tightening nut that provides tight fastening with a unique screw thread | Hacker News | 13:05 |
kanzure | "I'm a former mechanical engineer specializing in fastening (now I'm a Javascript developer)." | 13:05 |
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kanzure | damn that's a steep fall | 13:06 |
kanzure | http://jamesgolick.com/2013/5/19/how-tcmalloc-works.html | 13:06 |
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delinquentme | youll liked deze nuts https://www.youtube.com/watch?v=p8LGO68ZPlg | 13:51 |
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kanzure | .title | 14:04 |
yoleaux | Self-tightening nut that provides tight fastening with the aid of a unique screw thread #DigInfo - YouTube | 14:04 |
kanzure | legal docz https://swartzfiles.com/ | 14:14 |
kanzure | although none of them seem particularly new | 14:14 |
ebowden | paperbot: http://www.ncbi.nlm.nih.gov/pubmed/24071525 | 14:31 |
paperbot | http://libgen.org/scimag/get.php?doi=10.1016%2Fj.neuroimage.2013.09.038 | 14:31 |
ebowden | \:D/ | 14:32 |
ebowden | Apparently, 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 |
ebowden | So, people who show less cortical thinning in the later stages of development have higher increases in IQ. | 14:35 |
ebowden | I 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 |
delinquentme | ebowden, you're looking at your MRI scans or something? | 14:36 |
ebowden | Looking at the paper. | 14:36 |
delinquentme | "have a higher risk of developing lower IQ" lelz | 14:36 |
ebowden | Cognitive ability changes and dynamics of cortical thickness development in healthy children and adolescents. | 14:36 |
delinquentme | yeah but Im curious why you're excited about this | 14:37 |
delinquentme | or about specifically the thinning ... unless you've got it | 14:37 |
delinquentme | PS! IF ANYONE WANTS AN MRI .. i've got a friend in SF who needs volunteers | 14:37 |
delinquentme | 7 TSLA MRI | 14:37 |
ebowden | heh | 14:37 |
delinquentme | big fooker | 14:37 |
ebowden | Volunteers for what? | 14:37 |
delinquentme | brain scans | 14:37 |
ebowden | I guessed that much. | 14:38 |
ebowden | What experiment is he conducting? | 14:38 |
delinquentme | and rebar impailments | 14:38 |
delinquentme | ( fineprint) | 14:38 |
delinquentme | didn't ask | 14:38 |
delinquentme | and its a she | 14:38 |
ebowden | Ok. | 14:38 |
delinquentme | shes kinda cute | 14:38 |
delinquentme | but yeah I wanna maintain that conneciton .. so sending my friends hahah | 14:38 |
ebowden | I considered putting he/she, but thought it cumbersome. | 14:39 |
delinquentme | agreed | 14:39 |
delinquentme | ebowden> \:D/ | 14:39 |
delinquentme | scoliosis? | 14:39 |
ebowden | The \:D/ was because paperbot worked and spat out a working link to a delicious paper. | 14:40 |
delinquentme | true but your head is sideways | 14:41 |
* delinquentme concerned | 14:41 | |
ebowden | I find the findings exciting because it means there may be a potential path to treating and preventing an array of cognitive deficits. | 14:41 |
ebowden | heh | 14:41 |
streety | I hadn't realized until recently that there may be some risks with MRI. I had thought it was safe but expensive | 14:45 |
ebowden | Oh? | 14:45 |
streety | Would be nice to have an imaging modality that permitted safe serial scans over a lifetime | 14:45 |
streety | apparently some risk of DNA breaks | 14:46 |
delinquentme | issues associated with snapping every orbit of every electron in your body on and off ? | 14:46 |
delinquentme | I mean any folding / binding in your body happening within that time ... will be influenced ... no? | 14:46 |
streety | well when you put it like that . . . | 14:47 |
delinquentme | to a greater or less extending depending on the local attraction strength of the bonds | 14:47 |
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delinquentme | its fucking nuts that we can do that | 14:47 |
streety | It would be even better if it was something I could pull off in my garage | 14:53 |
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delinquentme | does your garage have a concrete bed? | 15:00 |
delinquentme | MRI = a few tons right? | 15:00 |
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nmz787_i | delinquentme: do you think a web-app that gave a person control of a FIB or SEM would make $$$? | 15:06 |
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kanzure | perhaps as a gimmick | 15:06 |
nmz787_i | delinquentme: 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_i | tour around some old IC | 15:06 |
nmz787_i | would have to be like $5 or $6 per minute | 15:07 |
nmz787_i | but I imagine there are a handful of people with that money and level of interest | 15:07 |
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streety | Building 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 |
ebowden | I 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 |
kanzure | https://news.ycombinator.com/item?id=8584719 | 15:30 |
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delinquentme | nmz787, its cool from a concept standpoint ... but like is this a perfectly functional FIB? | 15:56 |
delinquentme | adjustments / alignments could be a pain in the ass | 15:56 |
delinquentme | you gotta find the use case | 15:56 |
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delinquentme | streety, IDK if I'd build an MRI ... but I suppose you could ... | 16:00 |
delinquentme | https://www.youtube.com/watch?v=zksVZCJajCI | 16:01 |
streety | was that link for me? https://www.youtube.com/watch?v=hF3V-GHiJ78 seems more relevant | 16:05 |
delinquentme | haha streety so you know of him ! | 16:07 |
streety | one of those people I repeatedly rediscover | 16:08 |
streety | certainly worked on some interesting projects | 16:09 |
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delinquentme | so fucking nuts. https://www.facebook.com/video.php?v=754452984609528 | 16:20 |
delinquentme | im sweating. | 16:23 |
kanzure | .title | 16:24 |
yoleaux | hookgrip | Facebook | 16:24 |
nmz787_i | delinquentme: 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 window | 16:37 |
nmz787_i | and working on an arduino-controlled mouse for the machine | 16:38 |
nmz787_i | so 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 newbs | 16:39 |
delinquentme | https://www.youtube.com/watch?v=ZQUTJjWvx3I | 16:43 |
delinquentme | some of my fav | 16:43 |
delinquentme | nmz787, do you know andrew zoneneberg? | 16:43 |
delinquentme | hes building out something sim lar | 16:43 |
delinquentme | " yell racial slurs from a moving vehicle " ... " then get out " | 16:44 |
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delinquentme | OHHHHHHH BTW. | 17:49 |
delinquentme | interviewed with a CTO for a company around here ... asked him what were his experiences / practices around rebasing | 17:50 |
delinquentme | was clueless. | 17:50 |
catern | is rebasing a biology thing or are you talking about git | 17:50 |
delinquentme | ya . git | 17:50 |
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delinquentme | ERMERGER | 18:23 |
delinquentme | running. | 18:23 |
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nmz787_p | delinquentme: I internet-know him | 19:18 |
nmz787_p | I don't know of him modifying FIBs though, using them sure | 19:18 |
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delinquentme | heheheh nmz787 i internet-know 90% of my friends | 21:46 |
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delinquentme | geeeeze. so good https://www.youtube.com/watch?v=UwdLUuAjM9M&list=PLcghjaDFUHglje0wiMUDMTrUV6z5wGGQq&index=35 | 22:41 |
delinquentme | funk + 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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fenn | that DIY CT/x-ray scanner seems really useful for automated reverse engineering | 23:10 |
fenn | much better results than most laser scanners | 23:11 |
fenn | and you can probably do texture scanning at the same time, if you're into that sort of thing | 23:11 |
fenn | lots of noise though; i think his x-ray beam was not strong enough | 23:12 |
fenn | multiple exposure levels per angle would give you a higher dynamic range for things with both metal and organic materials | 23:13 |
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fenn | you can get near arbitrary resolution by having a larger screen and zooming in | 23:24 |
fenn | i saw a 3d reconstruction of a tick with synchrotron light, down to cellular resolution | 23:25 |
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fenn | omg CT images are so cool | 23:29 |
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fenn | .title http://www.nature.com/nature/journal/v442/n7103/fig_tab/nature04890_F1.html | 23:37 |
yoleaux | Figure 1 : Synchrotron X-ray tomographic microscopy of fossil embryos : Nature | 23:37 |
fenn | you might be able to read books without opening them, if they used iron based pigments | 23:41 |
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--- Log closed Tue Nov 11 00:00:47 2014 |
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