--- Log opened Wed Nov 18 00:00:28 2015 00:11 -!- ButaTine [FourFire@cm-84.215.195.59.getinternet.no] has joined ##hplusroadmap 00:13 -!- QuadIngi [FourFire@cm-84.215.195.59.getinternet.no] has quit [Ping timeout: 265 seconds] 00:31 -!- ArturShaik [~ArturShai@31.29.7.72] has quit [Ping timeout: 260 seconds] 01:03 -!- ArturShaik [~ArturShai@31.29.7.72] has joined ##hplusroadmap 01:09 -!- maaku [~quassel@botbot.xen.prgmr.com] has joined ##hplusroadmap 01:09 -!- maaku is now known as Guest8196 01:10 -!- Guest8196 is now known as maaku 01:19 -!- Hercules [Hercules@unaffiliated/genkei] has joined ##hplusroadmap 01:27 -!- poppingtonic1 [~Thunderbi@unaffiliated/poppingtonic] has joined ##hplusroadmap 01:29 -!- Hercules` [Hercules@103.59.249.189] has joined ##hplusroadmap 01:29 -!- poppingtonic [~Thunderbi@unaffiliated/poppingtonic] has quit [Ping timeout: 264 seconds] 01:29 -!- poppingtonic1 is now known as poppingtonic 01:32 -!- Hercules [Hercules@unaffiliated/genkei] has quit [Ping timeout: 272 seconds] 01:53 -!- Hercules` is now known as Hercules 01:53 -!- Hercules [Hercules@103.59.249.189] has quit [Changing host] 01:53 -!- Hercules [Hercules@unaffiliated/genkei] has joined ##hplusroadmap 02:08 -!- jtimon [~quassel@74.29.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 02:24 -!- Hercules [Hercules@unaffiliated/genkei] has quit [Disconnected by services] 02:24 -!- Hercules` [Hercules@103.59.249.189] has joined ##hplusroadmap 02:24 -!- Hercules` is now known as Hercules 02:24 -!- Hercules [Hercules@103.59.249.189] has quit [Changing host] 02:24 -!- Hercules [Hercules@unaffiliated/genkei] has joined ##hplusroadmap 02:31 -!- poppingtonic [~Thunderbi@unaffiliated/poppingtonic] has quit [Ping timeout: 240 seconds] 02:38 -!- Hercules [Hercules@unaffiliated/genkei] has quit [Read error: Connection reset by peer] 02:39 -!- Hercules [Hercules@unaffiliated/genkei] has joined ##hplusroadmap 03:18 -!- Madplatypus [uid19957@gateway/web/irccloud.com/x-ulakwbyrceyzedai] has quit [Quit: Connection closed for inactivity] 03:38 -!- ziggypup [~ziggypup@202-180-115-128.callplus.net.nz] has joined ##hplusroadmap 03:38 -!- ziggypup [~ziggypup@202-180-115-128.callplus.net.nz] has left ##hplusroadmap [] 03:46 -!- Hercules [Hercules@unaffiliated/genkei] has quit [Read error: Connection reset by peer] 03:47 -!- Hercules [Hercules@unaffiliated/genkei] has joined ##hplusroadmap 03:48 -!- Hercules [Hercules@unaffiliated/genkei] has quit [Client Quit] 04:04 -!- Hercules [~Hercules@unaffiliated/genkei] has joined ##hplusroadmap 04:07 -!- Hercules` [Hercules@117.228.235.63] has joined ##hplusroadmap 04:07 -!- Hercules [~Hercules@unaffiliated/genkei] has quit [Disconnected by services] 04:07 -!- Hercules` is now known as Hercules 04:07 -!- Hercules [Hercules@117.228.235.63] has quit [Changing host] 04:07 -!- Hercules [Hercules@unaffiliated/genkei] has joined ##hplusroadmap 04:09 -!- drewbot_ [~cinch@ec2-54-82-47-59.compute-1.amazonaws.com] has quit [Remote host closed the connection] 04:09 -!- drewbot [~cinch@ec2-23-20-152-70.compute-1.amazonaws.com] has joined ##hplusroadmap 04:14 < kanzure> .wik ricci surgery 04:14 < yoleaux> "In mathematics, the Poincaré conjecture (/pwɛn.kɑːˈreɪ/ pwen-kar-AY; French: [pwɛ̃kaʁe]) is a theorem about the characterization of the 3-sphere, which is the hypersphere that bounds the unit ball in four-dimensional space. The conjecture states:" — https://en.wikipedia.org/wiki/Poincar%C3%A9_conjecture 04:15 -!- Hercules` [Hercules@117.245.192.83] has joined ##hplusroadmap 04:19 -!- Hercules [Hercules@unaffiliated/genkei] has quit [Ping timeout: 276 seconds] 04:34 < kanzure> "we’re calling for applications through our website, http://sf.indiebio.co/ for those interested in a $250k funding package per startup and we’ll be funding 15 more companies in this batc" 04:34 < kanzure> *batch 04:36 -!- Hercules` [Hercules@117.245.192.83] has quit [Quit: Powered off :-)] 05:05 -!- Viper168_ [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 05:06 -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 246 seconds] 05:13 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-tqbmyuecnqyrcpza] has quit [Quit: Connection closed for inactivity] 05:19 -!- Darius [~quassel@cpe-158-222-160-123.nyc.res.rr.com] has joined ##hplusroadmap 05:40 -!- eudoxia [~eudoxia@r167-56-184-253.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 05:44 < kanzure> "Self-cleavage of fusion protein in vivo using TEV protease to yield native protein" http://www.ncbi.nlm.nih.gov/pubmed/15741334 05:45 < kanzure> "BASIC: A New Biopart Assembly Standard for Idempotent Cloning Provides Accurate, Single-Tier DNA Assembly for Synthetic Biology" http://pubs.acs.org/doi/abs/10.1021/sb500356d 05:46 < kanzure> "SELEX (Systematic Evolution of Ligands by EXponential Enrichment), as a powerful tool for deciphering the protein-DNA interaction space" http://www.ncbi.nlm.nih.gov/pubmed/21720957 05:46 < kanzure> "DNA-based binding motives for a substrate of choice is to be found using SELEX. Around that one would engineer the scaffold to hold functional peptides via DNA-binding domains. Naturally, a covalent binding would be better, maybe somebody has an idea for this. The DNA part of the structure would be more durable than regular enzymes. Peptide parts could be replaced constantly." 05:47 -!- fleshtheworld [~fleshthew@2602:306:cf0f:4c20:c4:2127:e85d:d6a2] has joined ##hplusroadmap 05:47 < kanzure> "Peptide nucleic acids are based on an amino backbone, they have higher binding affinity to DNA than DNA does, and you can conjugate peptides or proteins to them easily, albeit only in vitro." 05:47 -!- eudoxia [~eudoxia@r167-56-184-253.dialup.adsl.anteldata.net.uy] has quit [Quit: Leaving] 05:48 < kanzure> "Canonical genetic signatures of the adult human brain" http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.4171.html 05:49 < kanzure> "The structure and function of the human brain are highly stereotyped, implying a conserved molecular program responsible for its development, cellular structure and function. We applied a correlation-based metric called differential stability to assess reproducibility of gene expression patterning across 132 structures in six individual brains, revealing mesoscale genetic organization. The genes with the highest differential stability ... 05:49 < kanzure> ... are highly biologically relevant, with enrichment for brain-related annotations, disease associations, drug targets and literature citations. Using genes with high differential stability, we identified 32 anatomically diverse and reproducible gene expression signatures, which represent distinct cell types, intracellular components and/or associations with neurodevelopmental and neurodegenerative disorders. Genes in neuron-associated ... 05:49 < kanzure> ... compared to non-neuronal networks showed higher preservation between human and mouse; however, many diversely patterned genes displayed marked shifts in regulation between species. Finally, highly consistent transcriptional architecture in neocortex is correlated with resting state functional connectivity, suggesting a link between conserved gene expression and functionally relevant circuitry." 05:49 -!- atomical [~atomical@50.247.130.97] has joined ##hplusroadmap 05:50 < kanzure> "non-neuronal networks" what is the network then? 05:53 < JayDugger> Good morning. 05:54 < kanzure> "Unimolecular Submersible Nanomachines. Synthesis, Actuation, and Monitoring" http://pubs.acs.org/doi/abs/10.1021/acs.nanolett.5b03764 05:54 < kanzure> "... found using single molecule fluorescence correlation spectroscopy that only the molecules with fast rotating speed (MHz range) show an enhancement in diffusion by 26% when the motor is fully activated by UV light. This suggests that the USN molecules give ∼9 nm steps upon each motor actuation. A non-unidirectional rotating motor also results in a smaller, 10%, increase in diffusion. This study gives new insight into the light ... 05:54 < kanzure> ... actuation of motorized molecules in solution" 05:54 < kanzure> not sure how to use that 244-atom construction though. i guess you can throw on some chemical cages for delivery, but then why did you need the motor if you are relying on mostly diffusion? 05:55 < kanzure> "Instructing Perisomatic Inhibition by Direct Lineage Reprogramming of Neocortical Projection Neurons" http://www.cell.com/neuron/abstract/S0896-6273(15)00872-7 05:55 < kanzure> "Reprogrammed cortical callosal neurons acquire identity traits of corticofugal neurons; Induced corticofugal neurons receive increased input from PV+ cortical interneurons; Projection neuron class-specific identity instructs afferent inhibitory connectivity; ... During development of the cerebral cortex, local GABAergic interneurons recognize and pair with excitatory projection neurons to ensure the fine excitatory-inhibitory balance ... 05:55 < kanzure> ... essential for proper circuit function. Whether the class-specific identity of projection neurons has a role in the establishment of afferent inhibitory synapses is debated. Here, we report that direct in vivo lineage reprogramming of layer 2/3 (L2/3) callosal projection neurons (CPNs) into induced corticofugal projection neurons (iCFuPNs) increases inhibitory input onto the converted neurons to levels similar to that of endogenous ... 05:56 < kanzure> ... CFuPNs normally found in layer 5 (L5). iCFuPNs recruit increased numbers of inhibitory perisomatic synapses from parvalbumin (PV)-positive interneurons, with single-cell precision and despite their ectopic location in L2/3. The data show that individual reprogrammed excitatory projection neurons extrinsically modulate afferent input by local PV+ interneurons, suggesting that projection neuron class-specific identity can actively ... 05:56 < kanzure> ... control the wiring of the cortical microcircuit." 05:58 < kanzure> blocking PARP1 and upregulating/activating ATM kinase results in telomere lengthening ("ATM Kinase Is Required for Telomere Elongation in Mouse and Human Cells") http://www.cell.com/cms/attachment/2040375994/2053862741/mmc1.pdf http://www.cell.com/cell-reports/abstract/S2211-1247(15)01205-X?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS221112471501205X%3Fshowall%3Dtrue 06:00 < kanzure> "Scanning ultrasound removes amyloid-β and restores memory in an Alzheimer’s disease mouse model" http://stm.sciencemag.org/content/7/278/278ra33 06:01 < kanzure> "Three-dimensional bioprinting of embryonic stem cells directs highly uniform embryoid body formation" http://iopscience.iop.org/article/10.1088/1758-5090/7/4/044101/meta 06:01 < kanzure> "Engineering intracellular biomineralization and biosensing by a magnetic protein" http://www.nature.com/ncomms/2015/151102/ncomms9721/full/ncomms9721.html 06:02 < kanzure> "The Architecture of a Eukaryotic Replisome" http://www.nature.com/nsmb/journal/vaop/ncurrent/full/nsmb.3113.html 06:02 < kanzure> "At the eukaryotic DNA replication fork, it is widely believed that the Cdc45–Mcm2–7–GINS (CMG) helicase is positioned in front to unwind DNA and that DNA polymerases trail behind the helicase. Here we used single-particle EM to directly image a Saccharomyces cerevisiae replisome. Contrary to expectations, the leading strand Pol ε is positioned ahead of CMG helicase, whereas Ctf4 and the lagging-strand polymerase (Pol) ... 06:02 < kanzure> ... α–primase are behind the helicase. This unexpected architecture indicates that the leading-strand DNA travels a long distance before reaching Pol ε, first threading through the Mcm2–7 ring and then making a U-turn at the bottom and reaching Pol ε at the top of CMG. Our work reveals an unexpected configuration of the eukaryotic replisome, suggests possible reasons for this architecture and provides a basis for further ... 06:03 < kanzure> ... structural and biochemical replisome studies." 06:05 < kanzure> "Cooperative insertion of CO2 in diamine-appended metal-organic frameworks" http://science.energy.gov/bes/highlights/2015/bes-2015-07-b/ http://www.nature.com/nature/journal/v519/n7543/full/nature14327.html 06:07 -!- Aurelius_Work [~cpopell@209.48.69.2] has joined ##hplusroadmap 06:19 < kanzure> "Think of a random walk on an infinitely large chessboard; regardless of the fact that you cannot walk the entire board in finite time, the proportion of times you step on a white or black square depends only on the fraction of squares that are white and black. Similarly, if the total number of folds is small and regularly distributed it is not difficult to imagine independent, convergent discovery of two domains in the same fold by two ... 06:19 < kanzure> ... very distantly related sequences." 06:19 < kanzure> "The total number of possible folds is much more difficult to estimate than the total number of sequences. Survey of the existing protein universe reveals a total of ~800 folds (3), but as this represents only the existing sample of solved structures it is difficult to extrapolate from this number to the actual size of the entire fold universe. Attempts aimed at estimating the number of folds that have evolved on earth vary from 1000 to ... 06:19 -!- Darius [~quassel@cpe-158-222-160-123.nyc.res.rr.com] has quit [Remote host closed the connection] 06:20 < kanzure> ... 10,000 total folds, a discrepancy that highlights the difficulties inherent in these kinds of estimations (6, 19-24)." 06:21 < kanzure> from http://arxiv.org/pdf/q-bio/0603028.pdf 06:29 < fenn> "Transient opening of the blood-brain barrier results in activation of microglial cells, which then start engulfing amyloid plaques" 06:29 < fenn> i was wondering how ultrasound could affect amyloid plaque 06:29 < kanzure> "activation" 06:35 < thundara> fenn: http://stm.sciencemag.org/content/7/278/278ra33 ? 06:35 < fenn> well i don't see any images or article text or even an abstract 06:37 < kanzure> i wonder if there are any proteins that are "self-cleaving" once the amino acids exit the ribosome pore and fold for a bit. something like voluntarily removing a chunk of matter. 06:37 < thundara> feen: Paywall-removed http://jean.markov.codes/pub/278ra33.full.pdf 06:37 < fenn> oh, thank you 06:38 < thundara> No idea if it'd work in something the size of human brains, but given the complete lack of progress in AD, it's worth a try (And guessing the authors are going forward with it) 06:38 < kanzure> i was thinking there might be a way to use multiple ribosomes extruding amino acid sequences that combine in a way to more carefully control shape, instead of only a single amino acid sequence strand that folds on itself. however, the ribosomes would have to be positionally constrained to be in extremely close proximity and both would have to be working at roughly the same time. 06:40 < kanzure> (and the strands would have to partially fold at least to create functionality to seek out the nearby neighbor amino acid sequence strand and then cause the two strands to be positioned together in some useful way to influence some output shape) (but not sure whether this is more easily controlled than trying to control single-amino-acid-sequence folding) 06:41 < fenn> ribosomes are really big 06:41 < kanzure> specifically, i don't mean fusion proteins 06:41 < kanzure> or proteins with subdomains that combine with other proteins (this usually happens only after folding) 06:42 < fenn> you would have to have some kind of chaperone "tube" to convey the unfolded sequence to the center of your assemblage of ribosomes 06:42 < kanzure> maybe; but some proteins seem to be good at seeking out targeted small molecules, without the presence of a tube. 06:43 < fenn> i'm just saying the protein sequence usually folds immediately after it exits the ribosome, while the rest of the sequence is still being put together 06:43 < kanzure> i don't see any advantage of this multi-ribosome technique over "make proteins connect in known ways" 06:43 < thundara> fenn: Herp, broken file, fixed now 06:44 < kanzure> thundara: if you are asking whether you can transmit ultrasound into human brains through the skull, the answer is yes... 06:46 < thundara> kanzure: Well, there's two parts to that, the first is if it's as efficient (If you said yes or no, I'd believe it, I have no background here), the second is if there's actual therapeutic benefit 06:46 < kanzure> thundara: http://diyhpl.us/~bryan/papers2/neuro/ultrasound/ 06:47 < fenn> one advantage of multiple protein sequences being assembled into one structure is for extruding very large/long macrostructures that are covalently bonded, like for making a very long beta sheet without having to zig-zag? 06:48 < thundara> kanzure: Any favorites in there to start with? 06:48 < kanzure> that sounds like something that would work with protein-protein binding of separate substructures that combine into megastructure 06:48 < kanzure> i think protein-protein stuff sometimes uses covalent bonds 06:50 < kanzure> i was thinking of multi-ribosome because of inherent difficulty of imagining how to fold a piece of string to get an exact 3d shape, various problems like "oops you already visited that part of the graph" or "now you can't go back" in same way as plotting a path through a maze. but a second sequence strand can be whatever you want and can revisit certain regions based on molecular affinity push/pull over existing surface versus new amino ... 06:50 < kanzure> ... acid sequence "surface" you are extruding from the second ribosome. 06:51 < kanzure> "surface versus new" uh.. i mean "surface via new" 06:55 < kanzure> no results for "amino acid braiding" 06:56 < kanzure> .wik fusion protein 06:56 < yoleaux> "Fusion proteins or chimeric proteins (literally, made of parts from different sources) are proteins created through the joining of two or more genes that originally coded for separate proteins. Translation of this fusion gene results in a single or multiple polypeptides with functional properties derived from each of the original proteins." — https://en.wikipedia.org/wiki/Fusion_protein 06:57 < fenn> that's a joining of the DNA or RNA sequence 06:58 < kanzure> gah naming 06:58 < fenn> i don't think braiding is necessary because van der walls forces are large enough already between relatively straight overlapping segments 06:59 < kanzure> oh, agreed, i was just trying to think of names that someone else might have already used 07:00 < kanzure> .wik protein subunit 07:00 < yoleaux> "In structural biology, a protein subunit is a single protein molecule that assembles (or "coassembles") with other protein molecules to form a protein complex." — https://en.wikipedia.org/wiki/Protein_subunit 07:01 < kanzure> not helpful that ribosome itself has multiple subunits, makes for difficult searching 07:01 < fenn> this is kinda cool https://en.wikipedia.org/wiki/Collagen#Molecular_structure 07:02 < kanzure> "Three polypeptides coil to form tropocollagen. Many tropocollagens then bind together to form a fibril, and many of these then form a fibre." 07:03 < kanzure> oh right, biology people don't say braid they say helix -_- 07:03 < fenn> they're different things 07:04 < fenn> a braid is topologically halfway to being a knot 07:05 < kanzure> "Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy" http://www.sciencemag.org/content/336/6085/1171.short 07:06 < kanzure> "Structure of a designed protein cage that self-assembles into a highly porous cube" http://www.nature.com/nchem/journal/v6/n12/full/nchem.2107.html 07:11 < kanzure> "De novo protein design: how do we expand into the universe of possible protein structures?" http://www.sciencedirect.com/science/article/pii/S0959440X1500069X 07:11 < kanzure> see the figure under "Parametric protein designs achieved so far" 07:14 < kanzure> not very encouraging 07:16 < kanzure> here is a strange one, "Controlled Self-Assembly of Proteins into Discrete Nanoarchitectures Templated by Gold Nanoparticles via Monovalent Interfacial Engineering" http://pubs.acs.org/doi/abs/10.1021/acsami.5b02823 07:20 < kanzure> "Placing molecules with Bohr radius resolution using DNA origami" http://www.nature.com/nnano/journal/vaop/ncurrent/full/nnano.2015.240.html 07:25 < kanzure> yep not encouraging 07:58 -!- atomical [~atomical@50.247.130.97] has quit [Quit: My Mac has gone to sleep. ZZZzzz…] 08:00 -!- atomical [~atomical@50.247.130.97] has joined ##hplusroadmap 08:17 -!- c0rw|zZz is now known as c0rw1n 08:36 -!- sandeepkr [~sandeepkr@111.235.64.4] has quit [Ping timeout: 252 seconds] 08:56 -!- nmz787_i [~ntmccork@192.55.54.36] has joined ##hplusroadmap 09:00 -!- nzm [~nzm@104-5-115-27.lightspeed.sndgca.sbcglobal.net] has joined ##hplusroadmap 09:02 -!- zadock [~outsider@81.180.210.212] has joined ##hplusroadmap 09:07 -!- nzm [~nzm@104-5-115-27.lightspeed.sndgca.sbcglobal.net] has quit [] 09:12 < c0rw1n> i spose everyone's read it already but topical xkcd is topical https://xkcd.com/ 09:15 < kanzure> i think you mean http://xkcd.com/1605/ 09:18 < c0rw1n> yeah, the last one 09:20 < archels> mhm the final panel kindof takes the sting out of the argument by saying (and I paraphrase) "1000 times worse" 09:20 -!- zadock [~outsider@81.180.210.212] has quit [Quit: Leaving] 09:20 < archels> it's not 1000 times worse, it's a whole different playing field 09:20 < kanzure> machine code is wonderful, by comparison 09:29 -!- atomical [~atomical@50.247.130.97] has quit [Quit: My Mac has gone to sleep. ZZZzzz…] 09:32 -!- atomical [~atomical@50.247.130.97] has joined ##hplusroadmap 10:14 -!- lastfuture [~Peter@2a02:8071:b28c:9600:54f0:7336:b9da:dca1] has joined ##hplusroadmap 10:17 < nmz787_i> kanzure: am I correct to think git rebase dev would be different than git rebase origin/dev ? I'd guess the former means your latest local dev commit, while the latter means the latest local dev commit as origin sees it 10:18 < nmz787_i> so if I was already in dev, made some commits, then pull and merge some other peoples' commits, and wanted to rebase the merge away, I would be able to use the git rebase origin/dev to do this 10:18 < nmz787_i> otherwise, I won't commit to local dev, I'll git checkout -b someTempBranch then go back to dev, pull, go back to someTempBranch and rebase to dev, then merge someTempBranch into dev 10:19 < kanzure> "latest local dev commit as origin sees it" nope... it's "the latest local dev commit that your git repository knows about for the name origin/dev" 10:20 < kanzure> you have to run "git fetch origin" to update your local git repository's copy of whatever the remote "origin/dev" state actually is 10:20 < kanzure> yes, you should always be working with temporary branches to avoid debilitating blunders 10:21 < kanzure> you can also make a local branch that is a copy of origin/dev by a different name, like: git fetch origin && git checkout -b dev2 origin/dev; then you run git checkout and then type git rebase dev2 10:21 < kanzure> in general i recommend never using "pull" 10:22 < nmz787_i> hmm, ok, I will play it safe for now... I am at least comfortable with the temp-branch for rebasing 10:23 < nmz787_i> and yeah, I want to avoid headache filled blundering 10:37 < justanotheruser> the future of sysadmin involves Doom https://www.cs.unm.edu/~dlchao/flake/doom/ 10:42 -!- jenelizabeth [~jenelizab@cpc76802-brmb10-2-0-cust399.1-3.cable.virginm.net] has joined ##hplusroadmap 10:48 -!- abetusk [~abe@2601:184:4002:2290:7cc9:b4ce:fd1:455d] has quit [Ping timeout: 240 seconds] 11:01 -!- abetusk [~abe@2601:184:4002:2290:f0cf:c548:8055:2d0f] has joined ##hplusroadmap 11:02 -!- abetusk is now known as Guest72190 11:05 -!- ArturShaik [~ArturShai@31.29.7.72] has quit [Ping timeout: 272 seconds] 11:16 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-euvkvmjuxwizmrlm] has joined ##hplusroadmap 11:59 -!- kuudes [~kuudes@dsl-olubrasgw2-58c0c7-183.dhcp.inet.fi] has joined ##hplusroadmap 12:53 < kanzure> .title https://news.ycombinator.com/item?id=10588341 12:53 < yoleaux> When Software Eats Bio | Hacker News 13:01 -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has quit [Read error: Connection reset by peer] 13:07 -!- Viper168_ [~Viper@unaffiliated/viper168] has quit [Ping timeout: 246 seconds] 13:14 < archels> how the heck did I manage to introduce this Heisenbug in Python 13:14 < archels> if t > 0.0255: 13:14 < archels> import pdb;pdb.set_trace() 13:14 < archels> the whole thing works if those lines are there and I just keep hitting c 13:16 -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 13:20 < kuudes> memory leak error somewhere where otherwise something would write to a memory address over something else but importing and tracing causes word boundary alignment or similar and the thing gets just written to unallocated space or similar? 13:21 < kanzure> what's the error? 13:32 -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has joined ##hplusroadmap 13:55 -!- atomical [~atomical@50.247.130.97] has quit [Quit: My Mac has gone to sleep. ZZZzzz…] 14:09 -!- lastfuture [~Peter@2a02:8071:b28c:9600:54f0:7336:b9da:dca1] has quit [Quit: Bye bye baby] 14:50 -!- fleshtheworld [~fleshthew@2602:306:cf0f:4c20:c4:2127:e85d:d6a2] has quit [Read error: Connection reset by peer] 15:11 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-hauqpqdhpakkjiik] has joined ##hplusroadmap 15:39 < kanzure> what's the difference between http://ralphmirebs.livejournal.com/ and http://lana-sator.livejournal.com/ 15:41 -!- andytoshi [~andytoshi@wpsoftware.net] has quit [Changing host] 15:41 -!- andytoshi [~andytoshi@unaffiliated/andytoshi] has joined ##hplusroadmap 15:44 -!- jdqx [~jdqx@2602:306:cc94:1950:f514:1490:3bfb:a23c] has joined ##hplusroadmap 15:49 -!- Madplatypus [uid19957@gateway/web/irccloud.com/x-jfuggijmejamgqia] has joined ##hplusroadmap 16:38 -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 246 seconds] 16:58 -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 17:03 -!- Act [uid89656@gateway/web/irccloud.com/x-twnfkgumrurlzqzw] has quit [Quit: Connection closed for inactivity] 17:24 -!- jdqx [~jdqx@2602:306:cc94:1950:f514:1490:3bfb:a23c] has quit [Ping timeout: 240 seconds] 17:52 -!- Guest72190 is now known as abetusk 18:20 -!- TC [~talinck@66-161-138-110.ubr1.dyn.lebanon-oh.fuse.net] has joined ##hplusroadmap 18:20 -!- TC is now known as Guest23207 18:23 -!- nmz787_i [~ntmccork@192.55.54.36] has quit [Ping timeout: 250 seconds] 18:23 -!- poohbear [~poohbear@unaffiliated/tigger] has quit [Ping timeout: 250 seconds] 18:23 -!- enkiv2 [~john@c-24-60-31-0.hsd1.nh.comcast.net] has quit [Ping timeout: 250 seconds] 18:23 -!- hehelleshin [~talinck@66-161-138-110.ubr1.dyn.lebanon-oh.fuse.net] has quit [Ping timeout: 250 seconds] 18:23 -!- the8thbit [~8bit@66.186.100.194] has quit [Ping timeout: 250 seconds] 18:23 -!- xrr [~quassel@c21-76.uvn.zone.eu] has quit [Ping timeout: 250 seconds] 18:23 -!- JayDugger [~jwdugger@108.19.186.58] has quit [Ping timeout: 250 seconds] 18:24 -!- nmz787_i [ntmccork@nat/intel/session] has joined ##hplusroadmap 18:24 -!- poohbear [~poohbear@unaffiliated/tigger] has joined ##hplusroadmap 18:24 -!- xrr [~quassel@c21-76.uvn.zone.eu] has joined ##hplusroadmap 18:25 -!- the8thbit [~8bit@66.186.100.194] has joined ##hplusroadmap 18:25 -!- yashgaroth [~yashgarot@2602:306:35fa:d500:f5e0:f867:a11d:8d52] has joined ##hplusroadmap 18:25 -!- enkiv2 [~john@c-24-60-31-0.hsd1.nh.comcast.net] has joined ##hplusroadmap 18:25 -!- nmz787_i [ntmccork@nat/intel/session] has quit [Changing host] 18:25 -!- nmz787_i [ntmccork@nat/intel/x-jaqjyeygubdgucxe] has joined ##hplusroadmap 18:26 -!- sandeepkr [~sandeepkr@111.235.64.4] has joined ##hplusroadmap 18:33 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-euvkvmjuxwizmrlm] has quit [Quit: Connection closed for inactivity] 18:38 -!- JayDugger [~jwdugger@108.19.186.58] has joined ##hplusroadmap 18:43 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-hauqpqdhpakkjiik] has quit [Quit: Connection closed for inactivity] 19:02 -!- fleshtheworld [~fleshthew@2602:306:cf0f:4c20:d1e8:9477:46d:bb3d] has joined ##hplusroadmap 19:16 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-hbakcwityectofyv] has joined ##hplusroadmap 19:17 < kanzure> http://www.scientificamerican.com/article/china-s-bold-push-into-genetically-customized-animals/ 19:19 < kanzure> "scientists at Yunnan Key Laboratory of Primate Biomedical Research have used CRISPR to augment the neurological development of monkeys" 19:21 < kanzure> "If safety and efficacy issues can first be addressed, he is open to the future possibility of therapeutic uses, but not to eugenics. “In human beings CRISPR could be used to correct the mutation, which cause genetic human diseases, and it should not be used to generate any particular traits which some people may favor.”" 19:21 < kanzure> haha at people calling "favorable changes" the same thing as "eugenics" 19:22 < kanzure> people are awful 19:24 < JayDugger> I favor the trait of disease correction, 19:25 < andares> Popular figures aren't having mature conversations 19:25 < andares> It'll all be irrelevant when DIY becomes accessible, no? 19:26 < andares> Or will they make it some kind of felony? 19:26 < JayDugger> Yes to both? 19:26 < kanzure> "becomes accessible" what does that even mean? wtf 19:27 < kanzure> do you think the enzymes just evaporate when you touch them outside a lab? (well, they do, but you know what i mean) 19:30 < JayDugger> I assumed andares meant price points for equipment. 19:36 < kanzure> lotta people dump $20-$50k into random car hobbies and stuff, that's enough to cover most of the costs 19:38 -!- sandeepkr [~sandeepkr@111.235.64.4] has quit [Ping timeout: 250 seconds] 19:38 < andares> I meant mostly: < $100k, equipment is available to individuals and expertise required takes less than a couple years to master 19:38 < andares> Arbitrarily, basically 19:39 < andares> The point at which tens of thousands of people are doing it 19:39 < andares> Already aren't there some labs refusing to sell oligomers to private individuals? 19:40 < kanzure> equipment presently costs less than $100k as long as you either build it yourself or buy used equipment or buy equipment from something other than sigma aldrich or thermo fisheye 19:40 < kanzure> yes in general you should prefer to make your own dna 19:40 < andares> Can I get my hands on the equipment for that today? Or do I have to finish building the DNA printer? 19:41 < kanzure> you can buy used dna synthesizers on ebay for <$10k 19:41 < kanzure> but they probably wont work without some repair 19:41 < kanzure> which isn't so bad 19:41 < andares> Can I get things like RNA polymerase, tris etc. Delivered to my door? 19:42 < kanzure> probably, but i recommend purifying your own 19:42 < andares> Hrm, how do I do that? 19:43 < kanzure> http://diyhpl.us/wiki/diybio/faq 19:43 < kanzure> hmm reagent suppliers aren't listed- this would be a good thing for you to add 19:43 < kanzure> (it's a wiki) 19:43 < andares> Or perhaps a more practical question: has anyone here successfully done a transfection using all their own equipment at home yet? 19:44 < andares> I'm assuming too that once it becomes a big deal, the government will watch bio equipment like they watch chem equipment for the drug war 19:44 < andares> So eBay will be out of the picture 19:44 < kanzure> yes a few people in here have done transfection projects 19:44 < kanzure> ebay is always going to list biotech equipment from liquidation auctions etc 19:44 < kanzure> the government (specifically the fbi) has already been in contact with us 19:45 < kanzure> in particular this channel was assigned to their division of weapons of mass destruction 19:45 < kanzure> i took notes-- http://diyhpl.us/wiki/transcripts/fbi-diybio-2012/ 19:46 < kanzure> they are okay with diybio stuff existing as long as we report the freaks to them, e.g. the people planning genocides and such 19:47 < andares> That's awesome! (Re: successful transfection) 19:51 * andares waves at the nice federal agents 19:51 < andares> If only they could all be like Agent Cooper 19:51 < kanzure> they are armed, so don't touch your belt under any circumstances 19:51 * andares stops resisting 19:52 < kanzure> he said the word resist, get him 19:59 < kanzure> if you want to find particularly-friendly suppliers then i recommend searching the hplusroadmap logs for http://store.p212121.com/ or the same on https://groups.google.com/group/diybio 20:01 -!- sandeepkr [~sandeepkr@111.235.64.4] has joined ##hplusroadmap 20:06 -!- ArturShaik [~ArturShai@31.29.7.72] has joined ##hplusroadmap 20:08 -!- Madplatypus [uid19957@gateway/web/irccloud.com/x-jfuggijmejamgqia] has quit [Quit: Connection closed for inactivity] 20:18 < kanzure> 20:14 i am the "wumpus" of gnuradio 20:18 < kanzure> 20:16 i recognize "superkuh" and feel like i should know him but i can't place him 20:20 -!- sandeepkr [~sandeepkr@111.235.64.4] has quit [Ping timeout: 250 seconds] 20:22 -!- nmz787_i [ntmccork@nat/intel/x-jaqjyeygubdgucxe] has quit [Quit: Leaving.] 20:23 -!- docl [~docl@162.243.233.44] has joined ##hplusroadmap 20:23 < superkuh> rtlsdr stuff probably. Plus I talk/idle in #gnuradio and every other amateur radio channel. 20:33 -!- sandeepkr [~sandeepkr@111.235.64.4] has joined ##hplusroadmap 20:36 -!- sandeepkr [~sandeepkr@111.235.64.4] has quit [Max SendQ exceeded] 20:37 -!- sandeepkr [~sandeepkr@111.235.64.4] has joined ##hplusroadmap 20:43 < docl> How powerful is crispr? From what I've been reading in the news lately, it can do darn near anything (in terms of editing the genome), super cheap. Is this hype? 20:48 -!- fleshtheworld [~fleshthew@2602:306:cf0f:4c20:d1e8:9477:46d:bb3d] has quit [Disconnected by services] 20:48 -!- fleshtheworld- [~fleshthew@2602:306:cf0f:4c20:d1e8:9477:46d:bb3d] has joined ##hplusroadmap 20:52 < justanotheruser> http://www.scientificamerican.com/article/china-s-bold-push-into-genetically-customized-animals/ 20:52 < justanotheruser> .title 20:52 < yoleaux> China's Bold Push into Genetically Customized Animals - Scientific American 20:52 < justanotheruser> docl: funny, is that why you mentioned it? 20:53 < docl> Not just that article, there's been a lot of them lately. 20:53 < justanotheruser> or is this just baader meinhof phenomenon 20:53 < docl> http://www.newyorker.com/magazine/2015/11/16/the-gene-hackers 20:54 < justanotheruser> never heard of it before 20:54 < justanotheruser> before I read the article then saw you mention it within 2 minutes 20:54 < docl> I think it's just a super hot topic lately? 20:55 < justanotheruser> appears so http://www.google.com/trends/explore#q=crispr 20:55 < docl> http://www.nytimes.com/2015/11/15/magazine/the-crispr-quandary.html?_r=0 20:58 < docl> I've been wondering a lot about the idea of adapting mammals to cryogenic conditions. Normal mammals don't have a chance of surviving cryonics, but if we could introduce genes for cryoprotectant synthesis or import proteins into every cell, it might actually be possible. 20:59 < docl> If crispr is able to deliver precisely targeted genetic alterations to every cell of the body, you might even see a cryonics tolerance gene therapy for humans at some point. 21:18 -!- nmz787_i [~ntmccork@192.55.54.42] has joined ##hplusroadmap 21:21 -!- jrayhawk [~jrayhawk@unaffiliated/jrayhawk] has quit [Ping timeout: 244 seconds] 21:21 -!- heath_ [~heath@unaffiliated/ybit] has quit [Ping timeout: 260 seconds] 21:22 -!- kanzure [~kanzure@unaffiliated/kanzure] has quit [Ping timeout: 240 seconds] 21:30 -!- heath [~heath@unaffiliated/ybit] has joined ##hplusroadmap 21:35 -!- jrayhawk [~jrayhawk@unaffiliated/jrayhawk] has joined ##hplusroadmap 21:38 -!- gnusha [~gnusha@unaffiliated/kanzure/bot/gnusha] has quit [Ping timeout: 260 seconds] 21:45 -!- gnusha [~gnusha@unaffiliated/kanzure/bot/gnusha] has joined ##hplusroadmap 21:45 -!- Topic for ##hplusroadmap: biohacking, nootropics, transhumanism, open hardware | sponsored by lobsters everywhere, banned by the Federal Death Administration (5 times) | this channel is LOGGED: http://gnusha.org/logs | http://diyhpl.us/wiki | "ray kurzweil is a pessimist" - george church 21:45 -!- Topic set by kanzure [~kanzure@unaffiliated/kanzure] [Wed May 20 12:46:25 2015] 21:45 [Users ##hplusroadmap] 21:45 [ abetusk ] [ BobaMa ] [ enkiv2 ] [ juri_ ] [ p4nd4 ] [ strages ] 21:45 [ altersid ] [ btcdrak ] [ erasei ] [ justanotheruser] [ panax ] [ streety ] 21:45 [ amiller_ ] [ Burninate ] [ fenn ] [ justinzero ] [ ParahSailin ] [ Stskeeps ] 21:45 [ andares ] [ ButaTine ] [ fleshtheworld-] [ juul ] [ pasky ] [ superkuh ] 21:45 [ andytoshi ] [ c0rw1n ] [ gnusha ] [ kanzure ] [ PatrickRobotham] [ Taek ] 21:45 [ archels ] [ catern ] [ Guest23207 ] [ kuudes ] [ pompolic ] [ TeMPOraL ] 21:45 [ ArturShaik ] [ crescendo ] [ heath ] [ m0b ] [ poohbear ] [ the8thbit ] 21:45 [ augur ] [ Daeken ] [ HEx1 ] [ maaku ] [ proofoflogic ] [ thundara ] 21:45 [ Aurelius_Home] [ docl ] [ iDavid ] [ Madars ] [ rancyd ] [ TMA ] 21:45 [ Aurelius_Work] [ Douhet ] [ indiebio ] [ mf1008 ] [ redlegion_ ] [ Viper168 ] 21:45 [ Bakkot ] [ dpk ] [ Jawmare ] [ midnightmagic ] [ ryankara1on ] [ vivi4 ] 21:45 [ balrog ] [ drethelin ] [ JayDugger ] [ nickjohnson ] [ sandeepkr ] [ xrr ] 21:45 [ berndj ] [ drewbot ] [ jenelizabeth ] [ night ] [ saurik_ ] [ yashgaroth] 21:45 [ bkero ] [ dustinm ] [ jrayhawk ] [ nmz787_i ] [ sivoais ] [ yoleaux ] 21:45 [ blueskin ] [ EnabrinTain] [ jtimon ] [ nsh ] [ souljack ] [ yorick ] 21:45 -!- Irssi: ##hplusroadmap: Total of 90 nicks [0 ops, 0 halfops, 0 voices, 90 normal] 21:45 -!- Channel ##hplusroadmap created Thu Feb 25 23:40:30 2010 21:45 -!- Irssi: Join to ##hplusroadmap was synced in 10 secs 21:45 -!- kanzure [~kanzure@bryan.fairlystable.org] has quit [Client Quit] 21:46 -!- kanzure [~kanzure@unaffiliated/kanzure] has joined ##hplusroadmap 21:54 -!- gnusha [~gnusha@unaffiliated/kanzure/bot/gnusha] has quit [Ping timeout: 240 seconds] 21:59 -!- gnusha [~gnusha@unaffiliated/kanzure/bot/gnusha] has joined ##hplusroadmap 21:59 -!- Topic for ##hplusroadmap: biohacking, nootropics, transhumanism, open hardware | sponsored by lobsters everywhere, banned by the Federal Death Administration (5 times) | this channel is LOGGED: http://gnusha.org/logs | http://diyhpl.us/wiki | "ray kurzweil is a pessimist" - george church 21:59 -!- Topic set by kanzure [~kanzure@unaffiliated/kanzure] [Wed May 20 12:46:25 2015] 21:59 [Users ##hplusroadmap] 21:59 [ abetusk ] [ BobaMa ] [ enkiv2 ] [ justinzero ] [ ParahSailin ] [ Stskeeps ] 21:59 [ altersid ] [ btcdrak ] [ erasei ] [ juul ] [ pasky ] [ superkuh ] 21:59 [ amiller_ ] [ Burninate ] [ fleshtheworld- ] [ kanzure ] [ PatrickRobotham] [ Taek ] 21:59 [ andares ] [ ButaTine ] [ gnusha ] [ kuudes ] [ pompolic ] [ TeMPOraL ] 21:59 [ andytoshi ] [ c0rw1n ] [ Guest23207 ] [ m0b ] [ poohbear ] [ the8thbit ] 21:59 [ archels ] [ catern ] [ HEx1 ] [ maaku ] [ proofoflogic ] [ thundara ] 21:59 [ ArturShaik ] [ crescendo ] [ iDavid ] [ Madars ] [ rancyd ] [ TMA ] 21:59 [ augur ] [ Daeken ] [ indiebio ] [ mf1008 ] [ redlegion_ ] [ Viper168 ] 21:59 [ Aurelius_Home] [ docl ] [ Jawmare ] [ midnightmagic] [ ryankara1on ] [ vivi4 ] 21:59 [ Aurelius_Work] [ Douhet ] [ JayDugger ] [ nickjohnson ] [ sandeepkr ] [ xrr ] 21:59 [ Bakkot ] [ dpk ] [ jenelizabeth ] [ night ] [ saurik_ ] [ yashgaroth] 21:59 [ balrog ] [ drethelin ] [ jrayhawk ] [ nmz787_i ] [ sivoais ] [ yoleaux ] 21:59 [ berndj ] [ drewbot ] [ jtimon ] [ nsh ] [ souljack ] [ yorick ] 21:59 [ bkero ] [ dustinm ] [ juri_ ] [ p4nd4 ] [ strages ] 21:59 [ blueskin ] [ EnabrinTain] [ justanotheruser] [ panax ] [ streety ] 21:59 -!- Irssi: ##hplusroadmap: Total of 88 nicks [0 ops, 0 halfops, 0 voices, 88 normal] 21:59 -!- Channel ##hplusroadmap created Thu Feb 25 23:40:30 2010 21:59 -!- Irssi: Join to ##hplusroadmap was synced in 14 secs 22:00 -!- fenn [~fenn@unaffiliated/fenn] has joined ##hplusroadmap 22:02 -!- nmz787 [~nmz787@unaffiliated/nmz787] has joined ##hplusroadmap 22:03 -!- heath [~heath@unaffiliated/ybit] has joined ##hplusroadmap 22:05 < kanzure> oof 22:09 -!- Madplatypus [uid19957@gateway/web/irccloud.com/x-lnmhpvbqbgksxann] has joined ##hplusroadmap 22:57 -!- nmz787 [~nmz787@unaffiliated/nmz787] has quit [Ping timeout: 265 seconds] 22:57 -!- heath [~heath@unaffiliated/ybit] has quit [Ping timeout: 260 seconds] 22:57 -!- kanzure [~kanzure@unaffiliated/kanzure] has quit [Ping timeout: 244 seconds] 22:57 -!- gnusha [~gnusha@unaffiliated/kanzure/bot/gnusha] has quit [Ping timeout: 276 seconds] 22:57 -!- gnusha [~gnusha@unaffiliated/kanzure/bot/gnusha] has joined ##hplusroadmap 22:57 -!- Topic for ##hplusroadmap: biohacking, nootropics, transhumanism, open hardware | sponsored by lobsters everywhere, banned by the Federal Death Administration (5 times) | this channel is LOGGED: http://gnusha.org/logs | http://diyhpl.us/wiki | "ray kurzweil is a pessimist" - george church 22:57 -!- Topic set by kanzure [~kanzure@unaffiliated/kanzure] [Wed May 20 12:46:25 2015] 22:57 [Users ##hplusroadmap] 22:57 [ abetusk ] [ BobaMa ] [ enkiv2 ] [ justanotheruser] [ panax ] [ streety ] 22:57 [ altersid ] [ btcdrak ] [ erasei ] [ justinzero ] [ ParahSailin ] [ Stskeeps ] 22:57 [ amiller_ ] [ Burninate ] [ fenn ] [ juul ] [ pasky ] [ superkuh ] 22:57 [ andares ] [ ButaTine ] [ fleshtheworld-] [ kuudes ] [ PatrickRobotham] [ Taek ] 22:57 [ andytoshi ] [ c0rw1n ] [ gnusha ] [ m0b ] [ pompolic ] [ TeMPOraL ] 22:57 [ archels ] [ catern ] [ Guest23207 ] [ maaku ] [ poohbear ] [ the8thbit ] 22:57 [ ArturShaik ] [ crescendo ] [ HEx1 ] [ Madars ] [ proofoflogic ] [ thundara ] 22:57 [ augur ] [ Daeken ] [ iDavid ] [ Madplatypus ] [ rancyd ] [ TMA ] 22:57 [ Aurelius_Home] [ docl ] [ indiebio ] [ mf1008 ] [ redlegion_ ] [ Viper168 ] 22:57 [ Aurelius_Work] [ Douhet ] [ Jawmare ] [ midnightmagic ] [ ryankara1on ] [ vivi4 ] 22:57 [ Bakkot ] [ dpk ] [ JayDugger ] [ nickjohnson ] [ sandeepkr ] [ xrr ] 22:57 [ balrog ] [ drethelin ] [ jenelizabeth ] [ night ] [ saurik_ ] [ yashgaroth] 22:57 [ berndj ] [ drewbot ] [ jrayhawk ] [ nmz787_i ] [ sivoais ] [ yoleaux ] 22:57 [ bkero ] [ dustinm ] [ jtimon ] [ nsh ] [ souljack ] [ yorick ] 22:57 [ blueskin ] [ EnabrinTain] [ juri_ ] [ p4nd4 ] [ strages ] 22:57 -!- Irssi: ##hplusroadmap: Total of 89 nicks [0 ops, 0 halfops, 0 voices, 89 normal] 22:57 !rajaniemi.freenode.net [freenode-info] channel trolls and no channel staff around to help? please check with freenode support: http://freenode.net/faq.shtml#gettinghelp 22:57 -!- Channel ##hplusroadmap created Thu Feb 25 23:40:30 2010 22:57 -!- Irssi: Join to ##hplusroadmap was synced in 12 secs 22:57 -!- fenn [~fenn@unaffiliated/fenn] has quit [Ping timeout: 260 seconds] 22:57 -!- fenn [~fenn@unaffiliated/fenn] has joined ##hplusroadmap 22:57 -!- kanzure [~kanzure@unaffiliated/kanzure] has joined ##hplusroadmap 22:58 < nmz787_i> sloof 22:59 < nmz787_i> andares: the-odin for supplies 23:04 -!- yashgaroth [~yashgarot@2602:306:35fa:d500:f5e0:f867:a11d:8d52] has quit [Quit: Leaving] 23:05 -!- nmz787 [~nmz787@unaffiliated/nmz787] has joined ##hplusroadmap 23:05 -!- heath [~heath@unaffiliated/ybit] has joined ##hplusroadmap 23:05 -!- Act [uid89656@gateway/web/irccloud.com/x-euwydqcaiqhnoyzr] has joined ##hplusroadmap 23:06 -!- nmz787_i [~ntmccork@192.55.54.42] has quit [Quit: Leaving.] 23:47 < andares> The odin? --- Log closed Thu Nov 19 00:00:29 2015