--- Log opened Tue Dec 30 00:00:03 2014 --- Day changed Tue Dec 30 2014 00:00 < maaku> you'd still have people and/or specialized, non-self-replicating machines extracting the profitable resources 00:00 < fenn> sure it's more efficient to build specialized machines 00:00 < maaku> terminology disconnect, of course you'd have all specialized machines 00:01 < nmz787> fenn: would those parts be able to be purchased from vxb, or would they need some custom fab work? 00:01 < maaku> i meant machines requiring high-precision which the remote stuff wouldn't be able to achieve 00:02 < maaku> but if all the supporting infrastructure could be done automated and remotely, then the launch requirements for e.g. resource extraction on the moon or NEO could be within the range achievable today (expendable Falcon Heavy), and turn a profit 00:02 < fenn> you should be able to purchase everything, but it can be 100x more expensive to buy a threaded rod with a bearing mount machined on the end vs machining one yourself 00:02 < maaku> it's the >= 1000 tons of supporting equipment that kills you 00:03 < fenn> nmz787: you won't be able to purchase the nut flexure (probably) 00:03 < fenn> but the screw will flex so it's not a big deal 00:04 < fenn> "One of the projects I’m working on currently is to develop a new set of senses for people.  The field’s loosely called “exosenses”, and right now we’re flying the idea of developing new senses using tactile feedback and a smartphone, immersing the mass of digital and networked information available through feedback.  With time this feedback becomes integrated, the stimulus becoming a 00:04 < fenn> new independent sense as real as any other. 00:04 < fenn> For now this is taking the form of an Android phone talking over 3G with Google Maps and interfacing to the body with a set of actuated solenoids on a belt.  Drop a waypoint or tag a reference, and Android constantly gives you feedback on the heading of the marker.  All without ever looking at a map or thinking, just feeling through your new sense." 00:05 < fenn> that was 3 years ago. he later got a grant from DARPA to develop tactile computer interfaces 00:18 -!- FourFire [~FourFire@109.179.63.79.tmi.telenormobil.no] has joined ##hplusroadmap 00:32 -!- qu-bit [~shroedngr@unaffiliated/barriers] has quit [Remote host closed the connection] 00:43 -!- FourFire [~FourFire@109.179.63.79.tmi.telenormobil.no] has quit [Ping timeout: 255 seconds] 01:16 < fenn> i was wrong earlier when i said 30x the voltage; it would be a lot more than that. the 30 layersrawr. temperature gradient 01:19 < fenn> the 30 layers each create a small temperature gradient; the voltage goes perpendicular to the temperature gradient 01:20 < fenn> in a thermoelectric stack at least 01:47 -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 244 seconds] 01:52 -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 01:58 -!- FourFire [~FourFire@195.139.18.158] has joined ##hplusroadmap 02:09 < fenn> kanzure you may be interested to know that merkle was in #bitcoin-wizards briefly 02:11 -!- Beatzebub [~beatzebub@d172-218-204-36.bchsia.telus.net] has quit [Quit: No calling card for the unsung bard] 02:42 -!- ebowden [~ebowden@CPE-124-187-233-85.lns2.dav.bigpond.net.au] has quit [Remote host closed the connection] 02:52 -!- ebowden [~ebowden@CPE-124-187-233-85.lns2.dav.bigpond.net.au] has joined ##hplusroadmap 02:55 < fenn> presumably asking about http://xk.io/2013/12/22/factum-exchange/ 03:02 -!- QuadIngi [~FourFire@195.139.18.158] has joined ##hplusroadmap 03:03 -!- FourFire [~FourFire@195.139.18.158] has quit [Ping timeout: 258 seconds] 03:06 -!- QuadIngi is now known as FourFire 03:12 -!- FourFire [~FourFire@195.139.18.158] has quit [Ping timeout: 244 seconds] 03:14 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 04:18 < delinquentme> https://dweet.io/get/latest/dweet/for/VendingTransactionData 04:18 < delinquentme> any idea what that "resource" might be? 04:24 -!- FourFire [~FourFire@185.7.192.138] has joined ##hplusroadmap 04:34 -!- eudoxia [~eudoxia@179.26.178.217] has joined ##hplusroadmap 04:43 -!- drewbot [~cinch@ec2-54-227-213-61.compute-1.amazonaws.com] has quit [Remote host closed the connection] 04:43 -!- drewbot [~cinch@ec2-54-91-138-113.compute-1.amazonaws.com] has joined ##hplusroadmap 04:51 -!- FourFire [~FourFire@185.7.192.138] has quit [Ping timeout: 244 seconds] 05:05 -!- Vutral [~ss@mirbsd/special/Vutral] has quit [Ping timeout: 291 seconds] 05:12 -!- Vutral [~ss@mirbsd/special/Vutral] has joined ##hplusroadmap 05:33 -!- Viper168_ [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 05:33 -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 245 seconds] 05:34 -!- FourFire [~FourFire@77.88.71.253] has joined ##hplusroadmap 05:51 -!- strangewarp_ [~strangewa@c-76-25-206-3.hsd1.co.comcast.net] has joined ##hplusroadmap 05:54 -!- strangewarp [~strangewa@c-76-25-206-3.hsd1.co.comcast.net] has quit [Ping timeout: 245 seconds] 05:58 -!- shannon [~shananana@unaffiliated/shannon] has joined ##hplusroadmap 06:01 -!- shannon [~shananana@unaffiliated/shannon] has quit [Quit: Leaving] 06:02 -!- shannon [~shananana@unaffiliated/shannon] has joined ##hplusroadmap 06:19 -!- delinquentme [~dingo@74.61.157.78] has quit [Ping timeout: 264 seconds] 06:26 -!- juri_ [~juri@vpn166.sdf.org] has quit [Ping timeout: 250 seconds] 06:33 -!- juri_ [~juri@vpn166.sdf.org] has joined ##hplusroadmap 06:53 < kanzure> fenn: can you give me evidence that merkle was in there? kthx 06:53 < kanzure> maaku: replicators are generally viable for many things 06:53 < kanzure> maaku: i think that nobody has a good (even theoretical) design yet 06:53 < kanzure> other than "steal some cells" 06:54 < shannon> i'm new to this ... 06:54 < shannon> kanzure, can you tell me what "hplus" means? 06:54 < shannon> h = human? 06:54 < maaku> fenn: I don't think that was really Ralph Merkle 06:54 < maaku> just like I doubt shannon is Claude Shannon 06:54 < maaku> :P 06:54 < eudoxia> kanzure: https://botbot.me/freenode/bitcoin-wizards/2014-12-30/?msg=28518173&page=2 06:55 < maaku> shannon: h+ is related to transhumanism. see e.g. http://hplusmagazine.com/ 06:55 -!- ebowden [~ebowden@CPE-124-187-233-85.lns2.dav.bigpond.net.au] has quit [Read error: Connection reset by peer] 06:55 < maaku> and yes, h == human/humanity 06:55 < kanzure> today's china spam: tungsten carbide and solar panels 06:55 < kanzure> maaku: hplusmagazine is the worst thing ever. i regret doing sysadmin things for them. 06:56 < kanzure> maaku: come on, who seriously thinks making a physical magazine in 2010 is a good business plan? 06:56 < kanzure> shannon: instead i suggest looking at http://diyhpl.us/wiki/declaration 06:56 < shannon> i am not claude shannon 06:56 < kanzure> or http://web.archive.org/web/20130709183013/http://www.maxmore.com/extprn3.htm 06:56 < shannon> kanzure, i didnt click anything because url shorteners make me itchy 06:56 < shannon> especially promoted on irc 06:56 < kanzure> hplusmagazine is not a url shortener 06:57 < kanzure> that is definitely not merkle 06:59 < kanzure> maaku: i don't even think freitas' proposals had "parts closure". although i think he had a thing where if you allow for insanely complex vitamin parts, he could self-replicate? 07:01 < kanzure> maaku: btw one of the things i did as director of r&d at humanity+ was setup that reprap prize. although i think the money never got dispersed after i left... oh well. 07:07 < shannon> kanzure, i read it 07:08 < shannon> the topic isnt new to me 07:08 < shannon> just this channel and hplus 07:08 < shannon> but thank you 07:10 < shannon> im kinda excited that there are whole channels of people on IRC who find the subject interesting 07:10 < eudoxia> well, just one channel, singular, this one 07:10 < shannon> i get into more the mind uploading exocomputer augmented reality AI kinda cyber stuff more than biological, but it's all endlessly fascinating to me 07:11 < shannon> cause it's part of how i like to imagine the future, the self, all that speculative stuff 07:11 < shannon> i noticed another, ##biohack 07:11 < shannon> and im sure there are others 07:11 < kanzure> there aren't 07:11 < shannon> there is if i say there is 07:11 < kanzure> ##biohack is just the finger magnet people 07:11 < kanzure> please do you really think i don't relentlessly stalk everyone 07:11 -!- Evoril [~Evoril@86-45-222-8-dynamic.agg2.crw.prp-wtd.eircom.net] has quit [Quit: Leaving] 07:11 < shannon> do you really think you know who i am? 07:12 * shannon waves her hand dismissively 07:12 < kanzure> hmm. 07:12 < shannon> 321 chat 07:12 < kanzure> why would i have to know who you are to know whether or not i know about ##biohack? 07:12 < shannon> you're confused about which assertion im really challenging 07:13 < shannon> if i tell you there are a bunch of unicorns in a cave on mars, are you going to talk shit 07:13 < shannon> 1) you've never been to Mars, how would you know? 07:13 < kanzure> well what unicorn evidence would you bring me? 07:13 < shannon> there's no onus on me to give you evidence of unicorns 07:13 < kanzure> what? 07:13 < shannon> have some faith motherfucker 07:13 < shannon> :) 07:14 < kanzure> you are a moron 07:14 < shannon> you're overly confident in your "knowledge" 07:14 < kanzure> all i said is evidence 07:14 < kanzure> this is not confidence 07:14 < shannon> you say there's this or that and you're the authority and i say pfft 07:14 < kanzure> you are playing a very dumb game 07:15 < shannon> this isn't a solo dance 07:15 < eudoxia> why does this channel attract so many easily-angered internet people 07:15 < shannon> i thought that was just all irc 07:15 < shannon> i'm easily angered i guess but i think my intention is just playful so i dfont really give a fuck 07:16 < kanzure> your intention is not playful 07:16 < shannon> again, HOW WOULD YOU KNOW 07:16 < kanzure> evidence 07:16 < kanzure> which is something you don't seem to understand :) 07:16 < shannon> assumin' motherfucker 07:16 < shannon> you get the outline figured out and you assume you have the shading down 07:17 < shannon> it's just your puny mind filling in the details for you based on a bunch of biases and bullshit 07:17 < kanzure> yes my claude e. shannon bias 07:17 < shannon> you see one red apple, assume all red fruits are apples 07:18 < shannon> i'm telling you, there are channels, plural, in which people talk about these things 07:18 < shannon> PLURAL 07:18 < archels> heh @ assuming diyhp.us is a URL shortner 07:18 < shannon> yeah i wasnt thinking about that one too hard 07:18 < kanzure> shannon: name them or shut up 07:18 < archels> ooh yes, that sounds interesting. do share 07:18 < shannon> as if i answer to you? godm the arrogance 07:19 < shannon> "if you don't present all evidence on commmand then you're a liar" 07:19 < kanzure> hey that is a good rule 07:19 < kanzure> i like that one 07:19 * shannon makes wanking motion 07:19 < shannon> afk 07:20 < archels> shannon: if you're genuinly interested in transhumanism, you would share it just for the cause :) 07:21 < shannon> first i have to figure out what yall are up to 07:21 < kanzure> all i can think of are: #diybio ##biohack #biopunk #lesswrong #sl4 #immortal #transhumanusmi #lw-bitcoin #lw-prog 07:21 < shannon> so i have to do my part and actually read the shit that i thought was other stuff 07:22 < shannon> then you should try other irc networks, duh 07:22 < kanzure> we pretend to build things and then complain 07:22 -!- cluckj [~cluckj@cpe-24-92-48-18.nycap.res.rr.com] has joined ##hplusroadmap 07:22 < shannon> so all you can think of is more than one, plural, thanks for QED 07:22 < shannon> let's move on :):):) 07:22 < kanzure> let's not 07:23 < shannon> alright. you're currently wasting my time. bye. 07:23 < kanzure> you already read those links? 07:26 < shannon> listen bru 07:26 < shannon> fuck off. 07:26 < kanzure> go on 07:31 < ParahSailin> paperbot: http://online.liebertpub.com/doi/pdf/10.1089/hgtb.2012.117 07:32 < kanzure> yeah paperbot hasn't been replying lately, for some reason 07:32 < kanzure> even on failure 07:32 < ParahSailin> im sorry paperbot that i am not a better father 07:33 < paperbot> it's okay 07:33 < ParahSailin> so what are some insane experimental drugs to dope pregnant women with to improve function of the baby? 07:34 < kanzure> can't go wrong with vegf! 07:34 < ParahSailin> start with low level racetam? 07:34 < cluckj> stop secretly drugging women 07:34 -!- Evoril [~Evoril@86-45-222-8-dynamic.agg2.crw.prp-wtd.eircom.net] has joined ##hplusroadmap 07:34 < kanzure> you should look at development stages per week 07:35 < kanzure> and then look at which cells are differentiating around this time 07:35 < kanzure> and then decide from there 07:35 < ParahSailin> ok, what should i dope at week 19 07:35 < kanzure> that thing already has eyebrows 07:35 < cluckj> cupcakes 07:35 < kanzure> neural tube closure happens at week 6 07:36 < kanzure> you better just abort and try again 07:37 < ParahSailin> i told her to keep doing that until we rolled a boy 07:37 < ParahSailin> wouldnt listen 07:37 < cluckj> jfc 07:37 < kanzure> honestly at this point any sort of neural-related drugs probably have the same efficacy in utero and out 07:38 < cluckj> ^ 07:38 < cluckj> ParahSailin, is it yours? 07:39 < ParahSailin> thats for the courts to decide 07:40 < cluckj> lol 07:40 < cluckj> congratulations 07:43 < ParahSailin> so moms of muscular dystrophy kids are begging to have their kids allowed to take this oligo exon-skipper drug, but havent just ordered from idt? 07:43 < kanzure> you should probably just focus on post-utero stuff 07:43 < cluckj> enjoy sleep while you can 07:43 < kanzure> er i doubt that oligos can be digested without denaturing? 07:44 < ParahSailin> well the drug is a phosphorodiamidate morpholino 07:44 < ParahSailin> so i guess idt doesnt make those, but they make lna's 07:49 < kanzure> i think that at this stage the brain is relatively ungyrified 07:50 < kanzure> would be nice to test fenn's ideas about absolute numbers of neurons 07:51 < kanzure> .title http://www.jneurosci.org/content/33/26/10802.short 07:51 < yoleaux> Cortical Gyrification Induced by Fibroblast Growth Factor 2 in the Mouse Brain 07:51 < kanzure> "However, the mechanisms of gyrus formation have been elusive. We show that ventricular injection of FGF2 protein at embryonic day 11.5—before neurogenesis and before the formation of intrahemispheric axonal connections—altered the overall size and shape of the cortex and induced the formation of prominent, bilateral gyri and sulci in the rostrolateral neocortex. We show increased tangential growth of the rostral ventricular zone ... 07:51 < kanzure> ... (VZ) but decreased Wnt3a and Lef1 expression in the cortical hem and adjacent hippocampal promordium and consequent impaired growth of the caudal cortical primordium, including the hippocampus." 07:52 < kanzure> "These data also suggest that the position of cortical gyri can be molecularly specified in mice. In contrast, a different ligand, FGF8b, elicited surface area expansion throughout the cortical primordium but no gyrification." 07:56 < maaku> kanzure: every two years or so I read an h+ magazine article and remember why I don't read h+ magazine 07:57 < eudoxia> every two years i check the site to see if it's finally gone out of business 07:58 < maaku> kanzure: I'm pretty sure the advanced automation for space had parts closure, although only in the shown-to-be-theoretically-possible-to-achieve-parts-closure sense 07:59 < kanzure> right... no actual list of manufacturing processes that have been tested. 08:00 < kanzure> "So far, several hypotheses have been put forward on the processes that underlie the normal gyrification in the foetal brain, such as genetic control (Rakic, 2004; Piao et al., 2004) supplying a protomap of sulcal roots (Re´gis et al., 2005), active growth of convolutions during gyrogenesis (Welker, 1990), differential growth of inner and outer cortical layers (Richman et al., 1975), cytoarchitectonic differentiation (Connolly, 1950), ... 08:00 < kanzure> ... cortical growth (Toro and Burnod; 2005) and tension from white matter axonal fibres (Goldman-Rakic and Rakic, 1984; Van Essen, 1997; Hilgetag and Barbas, 2005). Furthermore, as most observations relied on post-mortem foetal brains (Feess-Higgins and Laroche, 1987), the potential influence of epigenetic or prenatal and postnatal environmental factors is unknown. To deal with such issue, we recently implemented an approach to reliably ... 08:00 < kanzure> ... measure the normal cortical folding process in vivo in human premature newborns (Dubois et al., 2008), based on non-invasive magnetic resonance images (MRI) (Hu¨ppi and Inder, 2001) and dedicated post-processing tools (Hu¨ppi et al., 1998; Cachia et al., 2003)." 08:01 < kanzure> this is from http://www.unicog.org/publications/dubois_brain08.pdf 08:01 -!- Evoril [~Evoril@86-45-222-8-dynamic.agg2.crw.prp-wtd.eircom.net] has quit [Quit: Leaving] 08:02 -!- eudoxia [~eudoxia@179.26.178.217] has quit [Read error: Connection reset by peer] 08:02 -!- eudoxia [~eudoxia@r167-56-6-157.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 08:04 < kanzure> rs133885 might be a marker of mathematical (dis)ability 08:05 < kanzure> or uh MYO18B 08:05 < kanzure> "Carriers of the MYO18B risk-genotype displayed a significantly lower depth of the right intraparietal sulcus (involved in numerical processing in humans)" 08:11 < kanzure> " show that variation in KCTD8 (potassium channel tetramerization domain 8) is associated with brain size in female adolescents (rs716890, P = 5.40 × 10−09). " 08:11 < kanzure> "In exposed girls only, the KCTD8 locus explains up to 21% of variance." (exposed to maternal smoke) 08:12 < kanzure> although reduced growth due to toxins is not very relevant 08:13 < kanzure> .title http://www.sciencedirect.com/science/article/pii/S0092867413003498 08:13 < yoleaux> kanzure: Sorry, that doesn't appear to be an HTML page. 08:13 < kanzure> "Evolution of the mammalian brain encompassed a remarkable increase in size of the cerebral cortex, which includes tangential and radial expansion. Here, we identified the DNA-associated protein Trnp1 as a regulator of cerebral cortex expansion in both of these dimensions. Gain- and loss-of-function experiments in the mouse cerebral cortex in vivo demonstrate that high Trnp1 levels promote neural stem cell self-renewal and tangential ... 08:13 < kanzure> ... expansion. In contrast, lower levels promote radial expansion, with a potent increase of the number of intermediate progenitors and basal radial glial cells leading to folding of the otherwise smooth murine cerebral cortex. Remarkably, TRNP1 expression levels exhibit regional differences in the cerebral cortex of human fetuses, anticipating radial or tangential expansion. Thus, the dynamic regulation of Trnp1 is critical to control ... 08:14 < kanzure> ... tangential and radial expansion of the cerebral cortex in mammals." 08:14 < kanzure> ("Trnp1 Regulates Expansion and Folding of the Mammalian Cerebral Cortex by Control of Radial Glial Fate") 08:14 < kanzure> well there you go, now go find the regulatory networks around that 08:15 < kanzure> .title http://www.tandfonline.com/doi/abs/10.4161/cc.25999#.VKLPbAQA 08:15 < yoleaux> An Error Occurred Setting Your User Cookie 08:15 < kanzure> "The multi-subunit chromatin remodeling BAF complex controls different developmental processes. Using cortex-specific conditional knockout and overexpression mouse models, we have recently reported that BAF170, a subunit of the vertebrate BAF chromatin remodeling complex, interacts with transcription factor (TF) Pax6 to control cortical size and volume. The mechanistic basis includes suppression of the expression of Pax6 target genes, ... 08:15 < kanzure> ... which are required for genesis of cortical intermediate progenitors (IPs) and specification of late neuronal subtype identity. In addition, we showed that a dynamic competition between BAF170 and BAF155 subunits within the BAF complex during progression of neurogenesis is a primary event in modulating the size of the mammalian cortex." 08:15 * heath waves gm 08:16 < heath> i'm really proud to be part of this community, so much great information shared the past 24 hours :) 08:16 < kanzure> "Control of cerebral size and thickness" http://link.springer.com/article/10.1007/s00018-014-1590-7 08:16 < kanzure> paperbot: http://link.springer.com/content/pdf/10.1007%2Fs00018-014-1590-7.pdf 08:16 < kanzure> paperbot: http://link.springer.com/article/10.1007/s00018-014-1590-7 08:18 < kanzure> here, http://diyhpl.us/~bryan/papers2/neuro/Control%20of%20cerebral%20size%20and%20thickness.pdf 08:19 * heath is digging TSUTOMU NIHEI - BLAME! Log 58+59 08:21 < kanzure> "The selective influence of IPs on radial cortical growth and gyrification in primates has been challenged by Nonaka-Kinoshita et al. [94]. They have provided proof that a massive expansion of IPs is not sufficient to induce folding in transgenic mice overexpressing cyclin D4 to promote IP proliferation, but instead leads only to surface expansion. However, in the gyrencephalic cortex of ferret, which shows abundant presence of oRG, the ... 08:21 < kanzure> ... same manipulation causes both cortical surface area expansion and folding, indicating a specific contribution of oRGC over IPs in the radial complex organization in phylogenetically distinct species [94]. Moreover, the expanded set of oRG in iSVZ provided additional scaffold for the oRGC-neuronal progeny, also allowing lateral dispersion when reaching the CP. Overall, these findings support the view that the two types of ... 08:21 < kanzure> ... abventricular progenitors, IPs (in SVZ) and oRGC (in iSVZ/oSVZ), have specific functions in the expansion of surface versus radial thickness/folding, respectively, across the mammalian phylogeny [3, 41, 43] (Fig. 3)." 08:22 < kanzure> "Along the same lines, despite the scarce presence of oRGC in the lyssencephalic mouse brain [35, 36], the Götz laboratory have recently induced augmented radial cortical thickness and gyrification by manipulating the expression of the Trnp1 (TMF1-regulated nuclear protein 1) gene, which encodes for a DNA-binding protein [24, 25], controlling the cell proliferation [96]. In vivo manipulation of the Trnp1 expression level (normally high ... 08:22 < kanzure> ... in vRGCs and low in IPs/oRGC) disclosed specific effects in cortical architecture. Overexpression of Trnp1 promotes the NE/vRGC renewal and, accordingly, the tangential/lateral expansion of the cortical surface. Lowering the Trnp1 level causes radial expansion due to increased numbers of both IPs and oRGC in SVZ and folding of the lyssencephalic cortex. These interesting findings support the view that establishment of the capacity ... 08:23 < kanzure> ... for cortical folding during mammalian evolution may involve superimposed layers of cellular decisions including modulation of the pool size of not only oRGC but also IPs, as predicted in the IPs hypothesis [97]." 08:23 < kanzure> that is pretty neat 08:24 < kanzure> "Notably, targeted deletion of Cux2 leads to increased progenitor proliferation in SVZ and increased UL cortical density and cortical thickness [120]. In contrast, double disruption of POU3F2/POU3F3 in mice causes a dramatic reduction in cortical thickness due to the specific loss of UL neurons and defective neuronal migration [121–123]. The Nuclear Factor One B (Nfib) is expressed in both vRGCs and LL neurons [124]. Upon targeted ... 08:24 < kanzure> ... mutation of the Nfib gene, oRG progenitors and late basal progenitors are absent, the ULs become thinner, and later born UL neurons show delayed migration towards the CP, thus contributing to the reduction of cortical thickness [126]." 08:24 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-oejxcnqzbtwuyodj] has joined ##hplusroadmap 08:31 < kanzure> trnp1 http://www.uniprot.org/uniprot/Q6NT89 "Expression is detected in the ventricular zone and neuronal layers of the developing cerebral cortex at 12, 18 and 21 gestation weeks. Differences in regional expression seem to correlate with the process of gyrification of the cortex." 08:32 < kanzure> ah and rs6689941 08:32 -!- FourFire [~FourFire@77.88.71.253] has quit [Read error: Connection reset by peer] 08:32 -!- Merovoth [~Merovoth@gateway/tor-sasl/merovoth] has quit [Remote host closed the connection] 08:33 -!- FourFire [~FourFire@77.88.71.253] has joined ##hplusroadmap 08:36 < kanzure> .title http://www.ncbi.nlm.nih.gov/gene/388610 08:36 < yoleaux> TRNP1 TMF1-regulated nuclear protein 1 [Homo sapiens (human)] - Gene - NCBI 08:36 < kanzure> what's the database that lists out plausible regulatory mechanisms acting on some gene's expression profile? 08:38 -!- FourFire [~FourFire@77.88.71.253] has quit [Ping timeout: 258 seconds] 08:38 < kanzure> huh there are antibodies for it (C1orf225) 08:39 < kanzure> cool it's also available on the market http://www.abnova.com/protocol_pdf/DS_H00388610-P01.pdf 08:45 < kanzure> i think TMF1 would be the target http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?exdb=AceView&db=human&term=TMF1 08:46 < kanzure> "Finally proteins from this gene may be modulated by acetylation; phosphorylation, as detailed at PhosphoSite" 08:46 < kanzure> "The gene is also known as TMF1, TMF or ARA160, LOC7110. It has been described as TATA element modulatory factor, androgen receptor coactivator 160 kDa protein, androgen receptor-associated protein of 160 kDa" 09:02 -!- Merovoth [~Merovoth@gateway/tor-sasl/merovoth] has joined ##hplusroadmap 09:04 -!- eudoxia [~eudoxia@r167-56-6-157.dialup.adsl.anteldata.net.uy] has quit [Quit: Leaving] 09:12 -!- pete4242 [~smuxi@boole.london.hackspace.org.uk] has joined ##hplusroadmap 09:36 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has quit [Remote host closed the connection] 09:36 -!- ThomasEgi [~thomas@2a02:810b:33f:dc18:412:de75:febb:bb62] has joined ##hplusroadmap 09:36 -!- ThomasEgi [~thomas@2a02:810b:33f:dc18:412:de75:febb:bb62] has quit [Changing host] 09:36 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has joined ##hplusroadmap 10:24 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-oejxcnqzbtwuyodj] has quit [Quit: Connection closed for inactivity] 10:24 -!- Burnin8 [~Burn@pool-71-191-174-26.washdc.fios.verizon.net] has joined ##hplusroadmap 10:27 -!- Burninate [~Burn@pool-71-191-174-26.washdc.fios.verizon.net] has quit [Ping timeout: 244 seconds] 10:38 -!- Burn_ [~Burn@pool-71-191-174-26.washdc.fios.verizon.net] has joined ##hplusroadmap 10:41 -!- Burnin8 [~Burn@pool-71-191-174-26.washdc.fios.verizon.net] has quit [Ping timeout: 250 seconds] 10:44 -!- FourFire [~FourFire@77.88.71.253] has joined ##hplusroadmap 10:52 -!- delinquentme [~dingo@74.61.157.78] has joined ##hplusroadmap 11:06 < kanzure> "Generation of a retroviral construct for forced expression of Trnp1" http://core.kmi.open.ac.uk/download/pdf/11034136.pdf 11:06 < kanzure> "Forced expression of Trnp1 in vivo by in utero electroporation" 11:07 < kanzure> aww "C-terminal fusion of GFP to Trnp1 inhibits its DNA binding ability" 11:11 < kanzure> figure 25 on pdf page 68 is pretty neat 11:11 < kanzure> er, 69 11:12 < kanzure> " In this context, in 4 out of 10 shRNA electroporated embryos not only expansion but also folding of the neocortex was observed (Figure 25A to B’). This observation together with the increase in oRGs is consistent with previous reports on oRGs implicated in expansion and folding of the cortex (Lui et al., 2011 for review; Reillo et al., 2011). To examine the morphology of radial glia in these folded regions, shRNA electroporated ... 11:12 < kanzure> ... brains were examined by staining with the radial glia specific antibody RC2 (Figure 25C). Interestingly, radial fibers diverged as they entered the cortical plate resembling a fanned array that has been described in larger brains (see Lui et al., 2011). Figure 26 shows more examples of different expanded brains upon Trnp1 shRNA electroporation and compares nonelectroporated hemispheres to electroporated hemispheres of the same ... 11:12 < kanzure> ... section. " 11:14 < kanzure> now that's science 11:15 < kanzure> "Altogether, down regulation of Trnp1 leads to cortical expansion in a dual mode. First, low levels of Trnp1 induce the generation of basal progenitors thereby increasing the total number of neurons. Second, radial glia with low levels of Trnp1 are also capable of generating outer radial glial cells lacking a ventricular apical process thereby leading to regional expansion in another way resembling cortical folding of gyrencephalic ... 11:15 < kanzure> ... brains (see Model Figure 38)." 11:21 < kanzure> (page 90) "Analysis of genes differentially expressed upon knock down (A) or overexpression of Trnp1 (B) in the developing mouse cortex. Note that most of the differentially expressed genes are directly or indirectly involved in regulation of gene expression." 11:28 < kanzure> oh yeah, beta catenin 11:28 < kanzure> er, beta catenin 11:28 < kanzure> (page 96) 11:31 < kanzure> "It has previously been shown that astrocytes from the postnatal cerebral cortex (postnatal day 7) can be directly converted into functional neurons by forced expression of Ngn2 or Mash1/Dlx2 (Berninger et al., 2007; Heinrich et al., 2010). Trnp1 was induced and detectable in reprogrammed cells generated both from Ngn2 and Mash1 transduced astrocytes 14 days after infection only in reprogrammed cells, i.e. in neurons (data not shown). ... 11:31 < kanzure> ... Along this line, using chromatin immunoprecipitation our collaborator Francois Guillemot was able to detect Ngn2 as well as Mash1 to bind very closely to the proposed promoter region of Trnp1. This suggested that Ngn2 and Mash1 might directly regulate Trnp1 activity." 11:32 < ParahSailin> most chinese dont know the polite word for llama 11:35 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Ex-Chat] 11:35 < cluckj> I don't even know the dirty word for llama 11:41 < shannon> yama 11:46 < kanzure> optogenetic control over Trnp1 would be a very interesting project 11:46 < kanzure> would prolly have to be a Tnrp1 up/down regulator that has the optogenetic element, and not Trnp1 itself 11:47 < kanzure> ParahSailin: is in utero cerebral electroporation off the table? 11:48 < ParahSailin> in chinese theres an internet meme where a homophone of "fuck your mother" has supplanted "goat camel" as the word for llama 11:48 < cluckj> that's great 11:53 < shannon> it's a goaty looking camel i think 11:53 < shannon> a really small, furry giraffe 11:54 -!- QuadIngi [~FourFire@77.88.71.230] has joined ##hplusroadmap 11:56 -!- FourFire [~FourFire@77.88.71.253] has quit [Ping timeout: 255 seconds] 12:00 -!- QuadIngi [~FourFire@77.88.71.230] has quit [Ping timeout: 255 seconds] 12:33 < kanzure> i'm not hearing no 12:41 -!- Boscop_ [~me@178.73.219.153] has joined ##hplusroadmap 12:44 -!- Boscop [me@unaffiliated/boscop] has quit [Ping timeout: 250 seconds] 12:50 -!- Boscop_ [~me@178.73.219.153] has quit [Max SendQ exceeded] 12:53 -!- Boscop [me@unaffiliated/boscop] has joined ##hplusroadmap 12:54 -!- augur [~augur@c-71-57-177-235.hsd1.fl.comcast.net] has quit [Ping timeout: 240 seconds] 12:59 -!- augur [~augur@c-71-57-177-235.hsd1.fl.comcast.net] has joined ##hplusroadmap 13:01 -!- augur_ [~augur@c-71-57-177-235.hsd1.fl.comcast.net] has joined ##hplusroadmap 13:05 -!- augur [~augur@c-71-57-177-235.hsd1.fl.comcast.net] has quit [Ping timeout: 255 seconds] 13:09 -!- Boscop [me@unaffiliated/boscop] has quit [Read error: Connection timed out] 13:13 -!- Boscop [~me@unaffiliated/boscop] has joined ##hplusroadmap 13:20 -!- FAMAS [~FAMAS@182.48.84.41] has joined ##hplusroadmap 13:34 -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 13:35 -!- Viper168_ [~Viper@unaffiliated/viper168] has quit [Ping timeout: 244 seconds] 13:38 -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Max SendQ exceeded] 13:39 -!- eudoxia [~eudoxia@r186-50-238-246.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 13:40 -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 13:44 -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Max SendQ exceeded] 13:47 -!- Evoril [~Evoril@86-45-222-8-dynamic.agg2.crw.prp-wtd.eircom.net] has joined ##hplusroadmap 13:47 -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 13:49 -!- maaku [~quassel@173-228-107-141.dsl.static.fusionbroadband.com] has quit [Ping timeout: 256 seconds] 14:06 -!- maaku [~quassel@173-228-107-141.dsl.static.fusionbroadband.com] has joined ##hplusroadmap 14:06 -!- maaku is now known as Guest87632 14:06 -!- Evoril [~Evoril@86-45-222-8-dynamic.agg2.crw.prp-wtd.eircom.net] has quit [Read error: Connection reset by peer] 14:14 -!- Evoril [~Evoril@86-45-222-8-dynamic.agg2.crw.prp-wtd.eircom.net] has joined ##hplusroadmap 14:26 < kanzure> "Whole genome sequences of two octogenarians with sustained cognitive abilities" http://www.sciencedirect.com/science/article/pii/S0197458014007180 14:33 < kanzure> .wik enzyme replacement therapy 14:33 < yoleaux> "Enzyme replacement therapy (ERT) is a medical treatment replacing an enzyme in patients in whom that particular enzyme is deficient or absent." — http://en.wikipedia.org/wiki/Enzyme_replacement_therapy 14:33 < kanzure> "Usually this is done by giving the patient an intravenous (IV) infusion containing the enzyme. Enzyme replacement therapy is currently available for some lysosomal diseases: Gaucher disease, Fabry disease, MPS I, MPS II (Hunter syndrome), MPS VI and Glycogen storage disease type II." 14:50 < delinquentme> kanzoo 14:50 < delinquentme> gchat 15:01 -!- cluckj [~cluckj@cpe-24-92-48-18.nycap.res.rr.com] has quit [Ping timeout: 240 seconds] 15:02 < kanzure> .title http://media.ccc.de/browse/congress/2014/31c3_-_6369_-_en_-_saal_1_-_201412272145_-_ecchacks_-_djb_-_tanja_lange.html#video 15:02 < yoleaux> C3TV - ECCHacks 15:02 < kanzure> should've been "A gentle introduction to elliptic-curve cryptography" 15:20 < kanzure> Control of outer radial glial stem cell mitosis in the human brain http://www.sciencedirect.com/science/article/pii/S2211124714005609 15:21 < kanzure> "human fetal cortical slice cultures" isn't science great 15:25 < kanzure> "Treatment with a second, more potent and selective ROCK inhibitor, dimethylfasudil (1 μM), mimicked blebbistatin and Y-27632 treatment, reducing translocations without significantly affecting divisions (Figure 4A)." 15:28 -!- ebowden [~ebowden@CPE-124-187-233-85.lns2.dav.bigpond.net.au] has joined ##hplusroadmap 15:29 < kanzure> "Fasudil, the only clinically available ROCK inhibitor," 15:30 < kanzure> .title http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2701389/ 15:30 < yoleaux> Peripheral Delivery of a ROCK Inhibitor Improves Learning and Working Memory 15:31 < kanzure> "The half-life of hydroxyfasudil in humans has been estimated at between 5-7 hours (Hinderling et al., 2007) therefore we administered the drug dose each morning prior to behavioral testing. [...] Injections were given subcutaneously into the scruff of the neck." 15:33 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 15:34 < kanzure> blergh "Asahi Kasei sued Actelion in 2008 claiming the company acquired CoTherix Inc. to halt work on fasudil and protect profits for its competing product, Tracleer. Before the acquisition, CoTherix was developing fasudil with Asahi Kasei." 15:48 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Remote host closed the connection] 15:58 < fenn> dexter is dead 16:00 < heath> fenn: the cartoon, the tv series, or a pet of yours? 16:00 < fenn> .wik Christine Cavanaugh 16:00 < yoleaux> "Christine Josephine Cavanaugh (née Sandberg; August 16, 1963 — December 22, 2014) was a voice actress who had a distinctive speaking style and had provided the voice for a large range of cartoon characters." — http://en.wikipedia.org/wiki/Christine_Cavanaugh 16:00 < heath> aww 16:01 -!- pete4242 [~smuxi@boole.london.hackspace.org.uk] has quit [Remote host closed the connection] 16:04 < kanzure> "In 2003 he received the 15th annual Bristol-Myers Squibb Award for Distinguished Achievement in Neuroscience Research, a $50,000 award, which noted two of his hypotheses in particular. The first hypothesis is the radial unit hypothesis, that in the developing cerebral cortex the cells are created at the base of each column, and that each new cell migrates past its predecessors." 16:04 < kanzure> "According to Nature Medicine, his first experiments required "a special grant, nearly 200 rhesus monkeys and so much radioactive thymidine that manufacturers had to retool their entire production system to provide it." Rakic injected the monkeys' fetuses with radioactive thymidine at a particular time after conception. Only replicating cells took up the radioactive label, which enabled Rakic to trace the lineages of brain cells as they ... 16:04 < kanzure> ... were created. He and his team then sliced the brain of each monkey into 7,000 sections for the benefit of future researchers. Because he used a radiolabel that decays slowly, the slides should be useful for years, and have so far led to more than 24 papers.[5]" 16:05 < kanzure> from http://en.wikipedia.org/wiki/Pasko_Rakic 16:06 < kanzure> for the benefit of future researchersfor the benefit of humanity 16:06 < kanzure> oh look this lovely individual has a website http://rakiclab.med.yale.edu/ 16:13 < kanzure> here he is giving a short research overview https://www.youtube.com/watch?v=jeSh9t4aMa4 16:16 -!- cluckj [~cluckj@cpe-24-92-48-18.nycap.res.rr.com] has joined ##hplusroadmap 16:20 -!- erasmus [~esb@unaffiliated/erasmus] has joined ##hplusroadmap 16:25 < shannon> are you a medical scientist of a sort, kanzure? 16:25 < shannon> ive been reading the things youve been posting today and shannon no smart shannon no understand good 16:26 < kanzure> i have absolutely no qualifications of any kind 16:26 < fenn> today on IRC MD we'll be discussing how to inject radioactive nucleotides into your baby's brain 16:27 < kanzure> just fetus, fenn 16:27 < kanzure> don't raise expectations 16:27 < eudoxia> i think the show really jumped the shark after cluckj lost his license to practice IRC medicine 16:28 < shannon> heh 16:28 < shannon> kanzure, do you have a favorite subject or area of science, as an autodidacct? 16:28 < cluckj> technically it was stolen by my TWIN BROTHER who came back from the dead after falling down an elevator shaft 16:28 < kanzure> shannon: no 16:28 < fenn> neuroscience, obviously 16:29 < fenn> also he likes pokemon 16:29 < shannon> (i like to know a little about a lot of things but it took me a lot of reading to figure out what Tnrp1 is) 16:29 < kanzure> just some dna-binding protein 16:29 < shannon> i was guessing some kind of biological science of course, life science, medicine 16:29 < shannon> yeah 16:29 < shannon> but it was cool because i had to read a bunch of stuff to be able to understand the stuff you were posting 16:29 < shannon> so i went on a little adventure 16:29 < kanzure> this is a very boring story 16:29 < shannon> im sorry i was kind of a cunt to you this morning 16:30 < shannon> actually, wait, im not 16:30 < shannon> you're kind of a dick 16:30 < cluckj> hahaha 16:30 < fenn> let us all take inspiration from this individual's heartwarming story of perseverance 16:30 < shannon> if youre going to talk like a pretentious asshole, spell things correctly 16:30 < shannon> smdh 16:31 < eudoxia> there are no typos in fenn's message 16:31 -!- erasmus [~esb@unaffiliated/erasmus] has quit [Ping timeout: 244 seconds] 16:31 < eudoxia> buddy did anyone ever tell you it's rude to nerd-snipe people into looking for typos in text? 16:32 < shannon> :/ 16:32 < kanzure> you get points for looking stuff up but minus points for telling me this is unusual for you 16:32 < fenn> "My kids do not eat sorbet! They eat sherbet! And they pronounce it ‘sherbert!’ And they wish it was ice cream!" 16:32 < shannon> it's unusual for me to look up things related to biological science because my education, and interest in it, stopped at the very basic 16:33 < shannon> i think we will probably agree to disagree until you get chanfix to fix your shit and then you ban me 16:33 < kanzure> it's basically the only operational, programmable nanotechnology that we have at the moment 16:36 < fenn> Trnp1 is not even in wikipedia so probably nobody but this one lab has heard of it 16:36 < kanzure> right 16:37 < kanzure> and it is unlikely to be the only mitosis-related progenitor modulator 16:37 < kanzure> i'm sure there's all sorts of other random cytokines or myosins that are relevant :/ 16:37 < fenn> so have we figured out whether folding is actually important or not? 16:37 < kanzure> that's presently ambiguous 16:38 < kanzure> i think that people have been doing studies of average cortical surface areas versus cortical thickness 16:38 < kanzure> instead of taking the derivative of the curvature of the surface or something 16:38 < fenn> todo: archive www.serendip.brynmawr.edu 16:39 < kanzure> these people say cortical surface area predicts general cognitive ability, rather than cortical thickness http://diyhpl.us/~bryan/papers2/neuro/The%20genetic%20association%20between%20neocortical%20volume%20and%20general%20cognitive%20ability%20is%20driven%20by%20global%20surface%20area%20rather%20than%20thickness.pdf 16:39 < kanzure> naturally, the majority of mri/fmri studies about general cognitive ability and neuroanatomy have been looking at cortical thickness instead 16:39 < fenn> is thickness talking about the neural stack thickness or the sulci overall? 16:40 -!- Vutral [~ss@mirbsd/special/Vutral] has quit [Ping timeout: 245 seconds] 16:42 < fenn> i think surface area is not quite incorrect.. uh, it's the total number of connections that matters, and more minicolumns means more surface area, but some people have smaller minicolumns and thus more connections but a smaller surface area 16:43 < kanzure> downregulation of Trnp1 levels causes "radial expansion due to increased numbers of both IPs and oRGC in SVZ and folding of the lyssencephalic cortex." and "First, low levels of Trnp1 induce the generation of basal progenitors thereby increasing the total number of neurons. Second, radial glia with low levels of Trnp1 are also capable of generating outer radial glial cells lacking a ventricular apical process thereby leading to regional ... 16:43 < kanzure> ... expansion in another way resembling cortical folding of gyrencephalic brains." 16:43 < kanzure> there are some okay diagrams in that larger thesis (the one that did in utero electroporation to inject science in fetal cortices) for surface area, gyrification and curvature and stuff 16:43 < kanzure> i agree that the actual definitions here seem a little suspicious 16:44 < fenn> .tr :academese :upgoer 16:44 < yoleaux> fenn: Sorry, that command (.tr) crashed. 16:44 < kanzure> surely the actual curvature of the cell bodies doesn't matter at all 16:44 < kanzure> so then it's a question of packing 16:44 < kanzure> but then why is that not the same thing as thickness? 16:44 < fenn> they aren't talking about cell body surface area 16:44 < fenn> cortical sheet surface area 16:44 < kanzure> sure they are... the surface area is made up of something. 16:45 < fenn> bah you're stuck in some kind of "how long is the coast of england" problem 16:45 < kanzure> no, they are 16:45 < fenn> (i say it's not infinite) 16:46 < shannon> id ask them to define coast 16:46 < fenn> 1623 cm^3 fits my interpretation 16:46 < kanzure> "cortical thickness" is apparently intended to mean "number of neurons" 16:46 < fenn> cm^2 i mean 16:47 < kanzure> trnp1 paper/thesis has lots of useful diagrams http://diyhpl.us/~bryan/papers2/neuro/Identification%20and%20functional%20analysis%20of%20Trnp1%20-%20a%20novel%20DNA%20associated%20protein%20with%20a%20key%20role%20in%20neurogenesis.pdf 16:47 < kanzure> say page 21 16:48 < kanzure> figure 1a 16:48 < kanzure> ooh figure 3 on page 23 16:49 < kanzure> ("Different modes of neurogenesis during cortical development") 16:49 < kanzure> page 32 figure 4 "Differences in neocortical development of the rodent and human brain" 16:51 < kanzure> page 46 figure 12 has some colorful microphotographs of trnp1 expression 16:52 -!- Vutral [~ss@mirbsd/special/Vutral] has joined ##hplusroadmap 16:53 < kanzure> ah, page 69 and 70 figure 25 and 26 "Loss of Trnp1 induces folding of the murine developing neocortex" 16:53 < kanzure> arrows seem to be pointing at the folding/gyrification 16:53 < kanzure> "Note the folds that developed at the site of electroporation" yessss 16:54 < kanzure> well anyway, in those folds it certainly doesn't look like an increase in neurons to me 16:56 < kanzure> ah right, you can electroporate just one hemisphere and have the other one leftover as a sort of control 16:57 < fenn> this paper is 200 pages long 16:58 -!- sheena [~home@S0106c8be196316d1.ok.shawcable.net] has joined ##hplusroadmap 16:59 < kanzure> hmm i can't find the diagram i was thinking of 17:00 < fenn> it's mostly pictures though so that's something 17:00 < kanzure> what i am expecting is a diagram that shows how gyrification means more or less neurons, or the constraints on connectivity or something 17:00 < kanzure> like page 5 figure 3 http://diyhpl.us/~bryan/papers2/neuro/Control%20of%20cerebral%20size%20and%20thickness.pdf 17:02 < fenn> i think neuroscience in general would benefit from everyone putting their data in a common computer-parseable format 17:03 -!- Evoril [~Evoril@86-45-222-8-dynamic.agg2.crw.prp-wtd.eircom.net] has quit [Quit: Leaving] 17:03 < fenn> that diagram just shows how stuffing a bunch of neurons in the same place makes a bulge 17:04 * fenn squints 17:04 < fenn> yes it actually says "hell orange" 17:05 < kanzure> heh 17:05 < fenn> hmyea this is a "burnt sienna" hmph harrumph 17:07 < cluckj> ehehehe neural bulge 17:07 < kanzure> "stuffing a bunch of neurons" honestly the density seems similar to me 17:09 < fenn> yes that's why there's a bulge, there's more neurons being added but the density stays the same. they have to go somewhere so the whole thing bulges outwards 17:10 < fenn> the other possibility is that the radial glial cells are just growing longer 17:10 -!- poppingtonic [~poppingto@unaffiliated/poppingtonic] has joined ##hplusroadmap 17:12 < fenn> thats what 'downregulation of Trnp1 levels causes "radial expansion due to increased numbers of both IPs and oRGC in SVZ"' means 17:13 < kanzure> then what is "cortical thickness" 17:13 < fenn> it's ambiguous 17:16 -!- augur_ is now known as augur 17:16 < kanzure> argh 17:17 -!- rk[ohio] is now known as rk[ca] 17:17 < fenn> yep this is a pretty stupid proble 17:17 < fenn> m 17:18 < kanzure> " Panizzon et al. (2009) reported that surface area and cortical thickness are genetically uncorrelated" 17:19 < kanzure> here is someone's attempt at explaining cortical thickness http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2891595/bin/nihms166013f1.jpg 17:19 < kanzure> from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2891595/ 17:19 < kanzure> "Geometrical relationship between cortical thickness, surface area and grey matter volume. In the surface-based representation, the grey matter volume is a quadratic function of distances in the surfaces and a linear function of the thickness. In the volume-based representation, only the volumes can be measured directly and require partial volume-effects (not depicted) to be considered." 17:19 < fenn> http://www.brainvoyager.com/bvqx/doc/UsersGuide/CorticalThicknessAnalysis/MeasuringCorticalThicknessInVolumeSpace.html looks like the blue highlighted areas are the cortical plate itself, so the thickness would be measuring the plate only, not the sulci 17:19 < kanzure> why is "grey matter volume" represented by a point 17:20 < fenn> that is a terrible diagram kanzure 17:23 -!- Guest87632 is now known as maaku 17:23 < kanzure> .wik polymicrogyria 17:23 < yoleaux> "Polymicrogyria (PMG) is a developmental malformation of the human brain characterized by an excessive number of small convolutions (gyri) on the surface of the brain. Either the whole surface (generalized) or parts of the surface (focal) can be affected." — http://en.wikipedia.org/wiki/Polymicrogyria 17:24 < fenn> too many convolutions makes jack a dull boy 17:26 < fenn> or it might just be associated with cytomegalovirus damage 17:27 < kanzure> how is this a disease 17:28 < fenn> it's not a disease, it's a very vague description 17:28 < fenn> "The diagnosis of PMG is merely descriptive and is not a disease in itself, nor does it describe the underlying etiology or cause of the brain malformation." 17:29 < kanzure> yes but seizures for some reason? 17:29 < kanzure> i guess people with seizures get scans and sometimes they have more folding 17:29 < kanzure> so you have to write that down 17:29 < kanzure> whereas non-seizing meatbags don't get their brains scanned as often 17:30 < fenn> scan all the brains! 17:30 < fenn> gotta scan em all 17:32 < fenn> i think seizures are from improper inhibition, so maybe the seizures are caused by an excitatory cell type outnumbering the inhibitory cell types 17:33 < kanzure> oh, "multiple small gyri" instead of large gyri? 17:34 < fenn> right, but that seems to be a secondary effect of a thickened cortex (pachygyria) 17:34 < kanzure> pachygyria is "unusually thick gyri" http://www.candicelange.com/LIS%20grading%20pic.jpg 17:35 < fenn> this is just words being dumb again 17:35 < kanzure> yes 17:36 < fenn> in this image the cortex is unusually thick and there are more sulci/gyri than usual http://en.wikipedia.org/wiki/File:Polymicrogyria_arrows.JPG 17:38 < fenn> oh i used the word pachygyria wrong 17:38 < fenn> "PMG _may_resemble_pachygyria (a few "thick folds" - a mild form of lissencephaly)." 17:40 < kanzure> this is all stupid 17:41 < kanzure> so which one has more neurons here http://cercor.oxfordjournals.org/content/9/2/151/F1.expansion 17:42 < fenn> i'd guess C 17:43 < fenn> you need to have the correct proportions of neurons too, or you'll have seizures 17:45 < kanzure> "While the folding pattern in normal human brains is quite consistent and related to the way information is stored and organized, the gyrations don’t appear until about the sixth month of gestation. Prior to that time, the human fetal brain, like the brain of a developing mouse, is fairly smooth. Further development of the human brain involves an increase in the number of neurons and a subsequent increase in the structural cells and ... 17:45 < kanzure> ... folding." 17:45 < kanzure> "By examining existing pathology samples of human fetal neural tissue from 8–9-week and 17–18-week gestation, Götz’s team has now found that Trnp1 levels are already lower in the regions where folds are normally destined to form and high in other areas. Thus, many weeks before human fetal brains fold, coauthor Victor Borrell explains, the “instruction for something to occur” is already present laying the roadmap of the ... 17:46 < kanzure> ... baby’s brain." 17:48 < kanzure> oh wait, that might be ideologically motivated to be misinterpreting their results 17:48 < kanzure> nevermind 17:48 < fenn> it's consistent with their hypothesis 17:49 < kanzure> yes but it's reported on a religious website that goes on to make spurious claims 17:49 < fenn> is there a monkey version of this gene? seems inconvenient to get human fetal brain samples 17:49 < kanzure> there is a mouse version of this gene 17:50 < fenn> but mice dont have sulci/gyri 17:50 < fenn> maybe ferrets 17:50 < kanzure> mice have gyri when you downregulate tnrp1 17:50 < fenn> O RLY 17:51 < fenn> why did they do in-vivo electroporation instead of germline engineering? 17:51 < fenn> gah too many papers 17:52 < fenn> "identification and functional analysis of Trnp1" 17:52 < kanzure> http://diyhpl.us/~bryan/papers2/neuro/Identification%20and%20functional%20analysis%20of%20Trnp1%20-%20a%20novel%20DNA%20associated%20protein%20with%20a%20key%20role%20in%20neurogenesis.pdf 17:52 < ebowden> What was that experiment where they gave mice human-like cerebral cortexes? 17:52 < kanzure> when they say "murine brain" they really mean "mouse brain" 17:52 < kanzure> ebowden: trnp1 and beta-catenin experiments 17:52 < ebowden> Ah, yes. 17:52 < fenn> figure 25: loss of Trnp1 induces folding of the murine developing neocortex 17:53 < ebowden> Kanzure, did they find any effect on some areas of the animals' cognition? 17:53 < fenn> looks like they just chopped em up 17:53 < fenn> mouse stew 17:54 < kanzure> i believe that in the beta-catenin experiments they did not allow the mice to live 17:54 < ebowden> I'd like to see what Trnp1 loss might do to their behaviour and cognition. 17:54 < ebowden> Ah. 17:54 < kanzure> http://diyhpl.us/~bryan/papers2/neuro/Regulation%20of%20cerebral%20cortical%20size%20by%20control%20of%20cell%20cycle%20exit%20in%20neural%20precursors.pdf.png 17:55 < kanzure> see http://diyhpl.us/~bryan/papers2/neuro/Increased%20neuronal%20production,%20enlarged%20forebrains%20and%20cytoarchitectural%20distortions%20in%20beta-catenin%20overexpressing%20transgenic%20mice.pdf 17:55 < kanzure> and http://diyhpl.us/~bryan/papers2/neuro/Regulation%20of%20cerebral%20cortical%20size%20by%20control%20of%20cell%20cycle%20exit%20in%20neural%20precursors.pdf 17:55 < ebowden> HOLY SHIT this has a lot of citations. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2861485/ 17:57 < fenn> 582 17:58 < kanzure> "Protein measurement with the Folin phenol reagent" has like 200,000 references 17:58 < kanzure> er, citations 17:58 < kanzure> http://www.nature.com/polopoly_fs/7.21204.1414513456!/image/nature_top_100_papers_infographicV2_30.10.14.jpg_gen/derivatives/fullsize/nature_top_100_papers_infographicV2_30.10.14.jpg 18:00 < ebowden> Oh, it was 1487 citations. 18:02 < kanzure> fenn: they probably didn't want to edit genomes? 18:02 < fenn> "identification and functional analysis of Trnp1" figure 38 (p. 97) "High levels of Trnp1 enlarge the pool of stem cells leading to tangential expansion. ... Low levels of Trnp1 lead to the generation of basal progenitor cells that subsequently amplify the neuronal output. ... Low levels of Trnp1 also provoke the generation of outer radial glia ... leading to radial expansion of the cortex and 18:02 < fenn> ultimately result in folding" so it's both mechanisms at the same time, more cells taking up room and radial expansion. also mice with knockout Trnp1 would mess up the neural stem cell generation process in areas that are not folded 18:02 < kanzure> oh, your reason is better 18:03 < fenn> electroporation is site specific i guess 18:03 -!- erasmus [~esb@unaffiliated/erasmus] has joined ##hplusroadmap 18:03 < fenn> there must be a regulatory process that confines Trnp1 to certain locations, like turing patterns (as usual) 18:04 < fenn> is it time to write a wikipedia article 18:04 < kanzure> no, because wikipedia hates primary sources 18:04 < kanzure> and "not notable" 18:04 < fenn> huh 18:04 < fenn> what if i copy it to my blog first 18:05 < fenn> this seems pretty important to neuroscience 18:05 < ebowden> Maybe you could publish a paper on it. 18:06 < kanzure> i don't know, man 18:06 < kanzure> i guess the primary problem is that you would have to actually have a blog for that 18:06 < fenn> there's already a paper on it 18:06 < kanzure> how about pasting some text into diyhpluswiki 18:06 < fenn> how about pasting some text into wikipedia 18:07 < kanzure> i think that's against their rules 18:07 < fenn> maybe i can convince the author to donate figure 38 18:07 < kanzure> er i think one of these articles was released under a creative commons license 18:08 < kanzure> or the other one he coauthored 18:09 < fenn> who owns the copyright of a thesis? 18:11 < kanzure> might be the university, sometimes the student, usually it's listed on the document somewhere? 18:11 < fenn> "This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution and reproduction in any medium, provided the original author and source are credited." http://www.sciencedirect.com/science/article/pii/S0959438814000427?np=y 18:12 < fenn> fig. 3 is not as good but it'll do 18:13 -!- erasmus [~esb@unaffiliated/erasmus] has quit [Quit: Colloquy for iPhone - http://colloquy.mobi] 18:13 < fenn> heh "current opinion in neurobiology" very scientific 18:15 < kanzure> what do you think "tetrahedron letters" is? hehe 18:26 < fenn> ugh making a new article is a lot of work now 18:30 < fenn> rawr i have to use a real browser apparently 18:30 * fenn cringes in anticipation of swap hell 18:59 < kanzure> well? 19:01 < fenn> my progress so far https://en.wikipedia.org/wiki/User:Fennfoot/sandbox 19:02 < fenn> this picture and caption sucks, i'd much rather use the one by ronny stahl 19:03 -!- eudoxia [~eudoxia@r186-50-238-246.dialup.adsl.anteldata.net.uy] has quit [Quit: Leaving] 19:11 -!- lichen [~lichen@c-50-139-11-6.hsd1.or.comcast.net] has joined ##hplusroadmap 19:47 -!- sheena [~home@S0106c8be196316d1.ok.shawcable.net] has quit [Ping timeout: 240 seconds] 20:00 < kanzure> hmph 20:02 -!- erasmus [~esb@unaffiliated/erasmus] has joined ##hplusroadmap 20:20 -!- lichen [~lichen@c-50-139-11-6.hsd1.or.comcast.net] has quit [Quit: Lost terminal] 20:26 -!- erasmus [~esb@unaffiliated/erasmus] has quit [Ping timeout: 265 seconds] 20:31 -!- top4o [~chatzilla@93.152.162.95] has joined ##hplusroadmap 21:18 -!- erasmus [~esb@unaffiliated/erasmus] has joined ##hplusroadmap 21:18 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has quit [Ping timeout: 244 seconds] 21:24 -!- erasmus [~esb@unaffiliated/erasmus] has quit [Quit: Colloquy for iPhone - http://colloquy.mobi] 21:25 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has joined ##hplusroadmap 21:37 -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 258 seconds] 21:42 -!- augur_ [~augur@c-71-57-177-235.hsd1.fl.comcast.net] has joined ##hplusroadmap 21:44 < kanzure> hehe here's some new spam: "Dear Bryan, I hope you got our email for gestational surrogacy with self eggs in India with us." 21:44 < kanzure> "If you have any questions and queries please do write back to us. We will be glad to answer each and every, small or big questions you might have" 21:44 < kanzure> signed "Paul" but the "From" is "Rita Bakshi" haha 21:45 < kanzure> and "Seema Bajaj" 21:45 < kanzure> very strange 21:45 < kanzure> and his link goes to an "Account suspended" page :) https://drritabakshi.com/cgi-sys/suspendedpage.cgi 21:45 -!- augur [~augur@c-71-57-177-235.hsd1.fl.comcast.net] has quit [Ping timeout: 245 seconds] 21:45 -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 21:49 < kanzure> well, i might as well send questions back i guess 22:00 -!- Burn_ [~Burn@pool-71-191-174-26.washdc.fios.verizon.net] has quit [Read error: Connection reset by peer] 22:00 -!- Burn_ [~Burn@pool-71-191-174-26.washdc.fios.verizon.net] has joined ##hplusroadmap 22:10 < fenn> careful you might get an unwanted kid in the mail 22:27 < kanzure> i don't think that's how it works 22:38 -!- ebowden [~ebowden@CPE-124-187-233-85.lns2.dav.bigpond.net.au] has quit [Remote host closed the connection] 22:38 -!- augur [~augur@c-71-57-177-235.hsd1.fl.comcast.net] has joined ##hplusroadmap 22:41 -!- augur_ [~augur@c-71-57-177-235.hsd1.fl.comcast.net] has quit [Ping timeout: 255 seconds] 23:17 -!- ebowden [~ebowden@CPE-124-187-233-85.lns2.dav.bigpond.net.au] has joined ##hplusroadmap 23:17 < delinquentme> lel. 23:17 < delinquentme> kanzure, they're starting the island in the middle east? 23:17 < delinquentme> I thought korea would be the place for that 23:27 -!- juri_ [~juri@vpn166.sdf.org] has quit [Ping timeout: 258 seconds] 23:48 -!- ebowden [~ebowden@CPE-124-187-233-85.lns2.dav.bigpond.net.au] has quit [Remote host closed the connection] --- Log closed Wed Dec 31 00:00:08 2014