--- Log opened Mon Nov 10 00:00:46 2014
00:01 < 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.
00:02 < jrayhawk> though for humans that's s/mutants/epimutants/
00:08 < 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
00:09 < fenn> we can revise the research later once we figure out how to get people in "non pathological" situations
00:11 < 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
00:12 < fenn> ...in "the real world"
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00:23 < 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.
00:26 < jrayhawk> people working from sane null hypothesis jump ahead of the science by decades
00:27 < jrayhawk> hypotheses
00:32 < 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.
00:38 < fenn> but weston price had to trek all over the world just to find the mythical humans living in utopia
00:40 < 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.
00:41 < fenn> he was a bit out of his field... nutrition/biochem vs dentistry
00:41 < jrayhawk> Anthropology is even further out.
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00:43 < jrayhawk> It's nice that universities are getting EvoS programs for this sort of thing.
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00:48 < fenn> what does EvoS stand for?
00:49 < jrayhawk> Evolutionary Studies; a departmental cross-pollination effort.
00:49 < jrayhawk> "multidisciplinary" i guess is the usual term
00:51 < 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
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00:52 < fenn> evolution.binghamton.edu/evos/ also does a really bad job of explaining itself
00:58 < 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."
01:00 < 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
01:01 < 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?
01:02 < 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/
01:03 < 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
01:04 < fenn> oh jeez now you're saying lamarckian evolution is true?
01:04 < fenn> because of epimutations or something?
01:05 < 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
01:06 < jrayhawk> actually that's just a stupid line of questioning; speciation is really poorly defined
01:07 < 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
01:08  * fenn reads on lamarckism
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01:12 < 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.
01:13  * 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
01:14 < fenn> a central focus it never had for Lamarck himself."
01:15 < 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?
01:17 < Viper168> it's more a mutation happens that ends up giving some a longer neck, and those reproduce better
01:18 < 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
01:19 < 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
01:22 < 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"
01:23 < Viper168> I've seen no evidence genes can be directly altered by the environment
01:23 < jrayhawk> hahaha
01:25 < fenn> but what they really meant is "there's a big old guy on a cloud who thought real hard and magically *poof* life"
01:26 < 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?
01:27 < jrayhawk> christ, it's like i am being dragged back into a discussion with nmz
01:29 < 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
01:30 < 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-?
01:31 < 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
01:32 < 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
01:34 < fenn> i was thinking of histone acetylation, nevermind
01:34 < Viper168> you're tripping
01:35 < Viper168> what have you been smoking
01:36 < ebowden> Wait, did someone here think Lamarckism and epigenetics are the same thing?
01:37 < 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
01:39 < ebowden> I remember when I saw a creationist I knew of log into the biology channel and I was like "nooooooooooooooooooO!".
01:40 < 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
01:41 < 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.
01:42 < 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
01:43 < ebowden> Ah.
01:43 < ebowden> Woah.
01:44 < 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
01:45 < 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
01:46 < 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.
01:47 < 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?
01:48 < fenn> a tiger?
01:48 < ebowden> So we've a lot more religious fanatics.
01:48 < ebowden> No.
01:49 < 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
01:50 < 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
01:51 < 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
01:52 < Viper168> but much less often
01:52 < Viper168> the catholic school was especially strict
01:52 < Viper168> damn nuns
01:53 < 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
01:54 < 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
01:55 < 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
01:56 < 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"
01:57 < 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
01:58 < 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.
01:59 < 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.
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02:00 < Viper168> at a point a low becomes an obstacle yes
02:01 < 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.
02:02 < 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.
02:03 < 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
02:04 < 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.
02:05 < 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
02:06 < 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.
02:07 < 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
02:08 < 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
02:10 < 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.)
02:12 < 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
02:13 < 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
02:14 < 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
02:15 < 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?
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02:15 < fenn> is this the same technology as the zeptoliter evanescent waveguide stuff?
02:16 < 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
02:17 < 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
02:20 < fenn> like the grate on your microwave
02:21 < 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
02:28 < 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
02:29  * fenn ahem
02:31 < jrayhawk> man, that waveguide stuff is terrifying mad science
02:31 < fenn> terrifyingly clever
02:32 < fenn> so if their single molecule sequencing works, why don't we have a complete human genome yet?
02:36 < 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
02:37 < 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
02:38 < fenn> that ought to be long enough to piece together multiple repeat regions
02:39 < jrayhawk> http://blog.pacificbiosciences.com/2013/10/resolving-complex-regions-in-human.html
02:43 < 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")
02:44 < jrayhawk> i only accept grass-finished genomes
02:45 < fenn> arabidopsis Genome size: 124.6 Mb
02:45 < fenn> Sum of Contig Lengths: 124.57 Mb
02:46 < 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
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02:48 < fenn> i'm not that into genomics
02:49 < 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
02:54 < 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
02:56 < fenn> and that genome is different for every cell
02:57 < fenn> er.. nevermind about that last bit, each cell would have just a list of epi-SNP's
03:02 < fenn> seems like the only way to get a complete epigenome is to throw the whole human into a meat grinder
03:16 < 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.
03:18 < 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
03:19 < 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
03:20 < fenn> ugh nice armpit picture
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03:21 < fenn> http://scienceblogs.com/pharyngula/2010/08/12/blaschkos-lines/
03:22 < 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
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03:29 < 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??
03:31 < 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
03:35 < fenn> how is an entire chromosome inactivated?
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03:41 < fenn> i guess it gets covered with a huge blob of RNA and then methylated to death
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04:32 < fenn> hello chido
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04:44 < chido> fenn: hey
04:49 < fenn> chido can you make a stain to visualize human X-inactivation?
04:51 < fenn> context http://scienceblogs.com/pharyngula/2010/08/12/blaschkos-lines/
04:51 < fenn> and calico cats
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05:06 < fenn> oh well
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06:19 < chris_99> paperbot: http://link.springer.com/chapter/10.1007/11967668_16
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06:38 < kanzure> .title https://www.neuro.mpg.de/borst
06:39 < kanzure> (tungsten electrodes)
06:39 < yoleaux> kanzure: Sorry, that command (.title) took too long to process.
06:40 < kanzure> i guess i can't blame ebowden for being a moron anymore now that i know he's trapped in catholic school
06:42 < kanzure> fly connectome stuff https://www.neuro.mpg.de/30076/borst_p2
06:43 < 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."
06:44 < 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
06:46 < 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."
06:51 < kjskjskjs> I only learned on Friday that a scanning electron microscope actually only scans a point of the sample at a time
06:52 < 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
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06:52 < kjskjskjs> into an image
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06:53 < 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
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07:48 < kanzure> hm.
07:54 < FourFire> kanzure: are you signed up for cryo, or planning to?
08:02 < 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
08:03 < kragenjaviersita> heh
08:03 < kanzure> thanks to cognitive dissonance, you are already dead
08:03 < justanotheruser> pls
08:04 < 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
08:05 < justanotheruser> kragenjaviersita: 5/22 of those words require googling
08:05 < justanotheruser> actually 6
08:06 < yorick> we should strive to do better than that
08:07 < kragenjaviersita> i'm not sure googling will be enough
08:08 < 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
08:09 < kragenjaviersita> entering the lottery and not winning, for example
08:10 < 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?
08:11 < 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
08:12 < 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?
08:13 < 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
08:14 < 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.
08:15 < andytoshi> 7!
08:15 < kragenjaviersita> kanzure: also http://www.computerhistory.org/fellowawards/hall/bios/Ralph,Merkle/
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08:34 < 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?
08:35 < kanzure> *somewhere
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08:42 < kanzure> "test your frontend against a real api" http://reqr.es/ https://news.ycombinator.com/item?id=8582075
08:43 < kanzure> heath: ^
08:45 < kanzure> .title https://news.ycombinator.com/item?id=8583257
08:45 < yoleaux> Firefox Developer Edition | Hacker News
08:46 < 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?
08:49 < 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
08:50 < 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;
08:51 < kanzure> when john carmack asks for hydrogen-peroxide you better give it to him
08:52 < 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
08:53 < 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
08:54 < kragenjaviersita> (which is the reason for a similar problem here in Argentina)
08:54 < kragenjaviersita> anyway, labs aren't very price-sensitive
08:55 < 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?
08:56 < kragenjaviersita> yeah
08:56 < kragenjaviersita> presumably they were worried about peroxide eating somebody's face off and then having to pay damages
08:58 < kragenjaviersita> http://armadilloaerospace.com/n.x/Armadillo/Home/News?news_id=296 gives some details
08:59 < 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
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09:03 < 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
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09:05 < 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
09:10 < 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"
09:12 < archels> cyberpunk? https://www.youtube.com/watch?v=GNoOiXkXmYQ
09:14 < kanzure> .title
09:14 < yoleaux> Aerial Burton 3D display projects images into mid-air #DigInfo - YouTube
09:17 < kragenjaviersita> DigInfo looks like a really interesting channel
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09:48 < nmz787_i> is there a language that escapes spaces as #20  ?
10:08 < rak[1]> not that i know of, but i know of a language that doesn't escape spaces at all!
10:14 < kanzure> &nbsp;
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10:22 < chris_99> i'm not sure i buy this - http://idenux.com/
10:23 < 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."
10:28 < 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
10:30 < 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/
10:31 < chris_99> haha
10:31 < nmz787_i> http://gizmodo.com/what-an-intel-and-fossil-team-up-could-mean-for-smartwa-1631599430
10:32 < 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.'
10:33 < nmz787_i> 'As we reported earlier, 50 Cent and SMS Audio announced a new partnership with Intel this evening.'
10:33 < nmz787_i> lol
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10:33 < nmz787_i> I never imagined I might meet 50 cent... but now who knows
10:45 < archels> paperbot: http://iopscience.iop.org/0957-4484/24/47/475301/pdf/0957-4484_24_47_475301.pdf
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10:52 < kragenjaviersita> nmz787_i: &#x20;
11:02 < kanzure> nmz787_i: of course you will meet 50 cent
11:04 < kanzure> also you will become an honorary member of wu tang clan
11:05 < kanzure> (nsh first, though. he's been queued up for a while.)
11:07 < nsh> \o/
11:11 < kanzure> nsh: having an actual felony on your record might help your case with them
11:12  * 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
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12:46 < kanzure> hrm
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12:57 < 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
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13:05 < 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)."
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13:06 < kanzure> damn that's a steep fall
13:06 < kanzure> http://jamesgolick.com/2013/5/19/how-tcmalloc-works.html
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13:51 < delinquentme> youll liked deze nuts https://www.youtube.com/watch?v=p8LGO68ZPlg
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14:04 < kanzure> .title
14:04 < yoleaux> Self-tightening nut that provides tight fastening with the aid of a unique screw thread #DigInfo - YouTube
14:14 < kanzure> legal docz https://swartzfiles.com/
14:14 < kanzure> although none of them seem particularly new
14:31 < 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
14:32 < ebowden> \:D/
14:35 < 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.
14:36 < 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.
14:37 < 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
14:38 < 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
14:39 < ebowden> I considered putting he/she, but thought it cumbersome.
14:39 < delinquentme> agreed
14:39 < delinquentme> ebowden> \:D/
14:39 < delinquentme> scoliosis?
14:40 < ebowden> The \:D/ was because paperbot worked and spat out a working link to a delicious paper.
14:41 < 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
14:45 < 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
14:46 < 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?
14:47 < 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
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14:47 < delinquentme> its fucking nuts that we can do that
14:53 < streety> It would be even better if it was something I could pull off in my garage
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15:00 < delinquentme> does your garage have a concrete bed?
15:00 < delinquentme> MRI = a few tons right?
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15:06 < nmz787_i> delinquentme: do you think a web-app that gave a person control of a FIB or SEM would make $$$?
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15:06 < 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
15:07 < 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
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15:09 < 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)
15:12 < 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...
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15:30 < 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
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15:56 < 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
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16:00 < delinquentme> streety, IDK if I'd build an MRI ... but I suppose you could ...
16:01 < delinquentme> https://www.youtube.com/watch?v=zksVZCJajCI
16:05 < streety> was that link for me? https://www.youtube.com/watch?v=hF3V-GHiJ78 seems more relevant
16:07 < delinquentme> haha streety so you know of him !
16:08 < streety> one of those people I repeatedly rediscover
16:09 < streety> certainly worked on some interesting projects
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16:20 < delinquentme> so fucking nuts. https://www.facebook.com/video.php?v=754452984609528
16:23 < delinquentme> im sweating.
16:24 < kanzure> .title
16:24 < yoleaux> hookgrip | Facebook
16:37 < 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
16:38 < nmz787_i> and working on an arduino-controlled mouse for the machine
16:39 < 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
16:43 < 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
16:44 < delinquentme> " yell racial slurs from a moving vehicle " ... " then get out "
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17:49 < delinquentme> OHHHHHHH BTW.
17:50 < 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
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18:23 < delinquentme> ERMERGER
18:23 < delinquentme> running.
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19:18 < nmz787_p> delinquentme: I internet-know him
19:18 < nmz787_p> I don't know of him modifying FIBs though, using them sure
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21:46 < delinquentme> heheheh nmz787 i internet-know 90% of my friends
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22:41 < delinquentme> geeeeze. so good https://www.youtube.com/watch?v=UwdLUuAjM9M&list=PLcghjaDFUHglje0wiMUDMTrUV6z5wGGQq&index=35
22:57 < 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.
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23:10 < fenn> that DIY CT/x-ray scanner seems really useful for automated reverse engineering
23:11 < 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
23:12 < fenn> lots of noise though; i think his x-ray beam was not strong enough
23:13 < fenn> multiple exposure levels per angle would give you a higher dynamic range for things with both metal and organic materials
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23:24 < fenn> you can get near arbitrary resolution by having a larger screen and zooming in
23:25 < fenn> i saw a 3d reconstruction of a tick with synchrotron light, down to cellular resolution
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23:29 < fenn> omg CT images are so cool
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23:37 < 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
23:41 < fenn> you might be able to read books without opening them, if they used iron based pigments
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--- Log closed Tue Nov 11 00:00:47 2014