2014-12-24.log

--- Day changed Wed Dec 24 2014
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archelshttp://www.davidbrin.com/SKEPTICcontactperils.pdf00:46
archels200900:46
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archelshttps://www.youtube.com/watch?v=DTNY6aJ7jlo02:33
archelsokay, now someone do this with a head-mounted FLIR and overlaid augmented reality02:34
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JayDuggerarchels, that's fairly similar to the synthetic vision systems in modern business jets.04:06
JayDuggerNot head-mounted, but FLIR and AR overlay both apply.04:07
archelsnot familiar with those, do you have a link?04:14
archelslike a windscreen HUD?04:15
JayDuggerI am, no link, exactly like that with FLIR video projected on it.04:15
JayDuggerHang on...let me look for an image.04:15
JayDuggerhttps://flic.kr/p/6rKfE304:17
JayDuggerLike that, but with a second green video portion, a raster image from the FLIR. (That's a flight simulator, so the runway looks false.)04:18
JayDuggerhttp://www.flightglobal.com/assets/getasset.aspx?itemid=3932604:19
JayDuggerThat's a better image, but not of a real HUD. The AR overlays don't photograph that well.04:20
JayDuggerI know the previous image shows a real HUD's overlay.04:20
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archelshmm, that's not so much enhancing reality though as projecting some data on top of it04:22
archelswithout maitaining the spatial relation between the projected and the projected upon04:23
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JayDuggerWhat did you have in mind?04:26
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archelsI guess something a bit like this - http://www.magicvisionlab.com/pub/weir_ismar12/thumbnail.jpg - just a heatmap overlay on your visual field05:01
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kanzureasdf06:07
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FourFire?06:13
eudoxiaanother system definition facility06:14
kanzurehi eudoxia06:18
eudoxiahi kanz06:18
eudoxiaare you planning on starting an octopus farm to uplift octopuses06:18
eudoxiathrough selective breeding06:19
poppingtonicor iterated embryo selection?06:19
eudoxiamaybe it could even be automated06:20
kanzurewell that really depends on what you mean by planning06:20
eudoxialike a machine that uses a camera and computer vision to select embryos with large brains and eyes and automatically discards/lets them pass at a rate of thousands of babby octopuses an hour06:20
kanzureselecting for large eyes may not be a good idea06:21
archelss/uplift/upload/06:21
kanzurei dunno if there's anything to upload, they probably don't have much to say06:21
poppingtonichttp://www.nickbostrom.com/papers/embryo.pdf06:22
kanzureunfortunately since this is a bostrom article 80% of this file is going to be bullshit about how much i should hate myself for thinking about embryo selection at all06:24
poppingtonichaha06:24
poppingtonicthough i didn't actually see anything like that06:26
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eudoxiathere's a lot of other bullshit in that pdf though06:26
eudoxiawatermarks, instructions for the editor, "author query form", some other shit06:27
eudoxiajournals need to embrace minimalism06:27
kanzurejournalisms need to embrace "give bryan all the papers"ism06:27
kanzures/journalisms/journals06:28
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poppingtonic"Our analysis suggests that human embryo selection will not be a major factor in world affairs in the medium term unless either it becomes very widely adopted or IES becomes feasible and is used by a nontrivial minority. In either of those cases, however, it would significantly increase world human capital, and, in the case of IES, possibly create individuals with unprecedented levels of cognitive capacity."06:30
archels"Our analysis suggests that x will not be a major factor unless it becomes a major factor"06:31
kanzurearchels for president06:32
poppingtonicunless someone really really wants it to happen06:32
kanzureoctopus would be much easier to work with for those purposes06:35
cluckjkanzure, thx06:35
cluckjbeta cell transplants, which that basically is, only work for a short time before the immune system destroys them again06:36
kanzureyou could transform pre-existing cells06:36
kanzurefrom your body06:36
kanzurewhich should be immune-compatible06:36
cluckjbuuuuut if somatic cells are being transformed, you can just do it over and over again06:36
cluckjI think the immune response is targeting cells that produce insulin06:39
cluckjso those somatic cells that have been transformed would eventually be destroyed as well06:39
kanzurethere was another 2014 igem project about resetting certain acquired immunities06:41
cluckjhmm06:47
kanzuresee http://diyhpl.us/wiki/dna/projects/06:47
cluckjI really need to get my biohack on and see how I got T1 before I mess with anything06:47
cluckjwhen you get T1 at age 30, there are multiple possible causes06:47
cluckjit's probably genetic predisposition + viral infection06:48
cluckjI asked my endocrinologist if we could run some genetic tests and he said it wasn't worth the money06:48
kanzure"you are a worthless human being"06:48
kanzure"wtf is a genetic test?"06:49
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cluckjlol06:49
cluckjhe was looking at it from a clinical standpoint, where the kind of T1 I had would really have no effect on my treatment06:50
cluckjhe's right in that regard because he has no idea about the biohax06:50
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cluckjonce the baby is old enough I will be able to get back to genspace and do some genetic testing06:54
kanzurehuman vitamin c synthesis by stealing a gene from lemurs http://2014.igem.org/Team:UST_Beijing/Project07:01
cluckjyesss07:03
kanzurehttp://2014.igem.org/Team:Cambridge-JIC "Marchantia polymorpha is our novel, eukaryotic multicellular chassis. Being a liverwort, it is one of the most primitive land plants around. Its small size and relative genetic simplicity make it easy to work with and an exciting new model organism in synthetic biology. Content to grow on agar plates, marchantia can be bioengineered in a standard lab with minimal extra equipment."07:29
cluckj"primitive"07:31
archelskanzure: how far are we with retroviral therapy on humans?07:37
kanzurebacterial explosives remediation of TNT and nitroglycerin http://2014.igem.org/Team:Exeter/Project07:38
archelsbe it in the clinic, in hackerspaces or in Russia07:38
kanzurearchels: well we have stuff that works, but nobody wants to use it or something07:38
archelsnot even the biohackers? c'mon07:39
cluckjit's not like anybody has died from retroviral therapy or anything...07:40
kanzurethis is interesting, optical control of the genetic expression of a specific receptor, where each different receptor allows a different virus with genetic payloads to enter the cell http://2014.igem.org/Team:Freiburg/Project/Overview07:41
kanzureprotein complements as biosensors of protein activity in cells http://2014.igem.org/Team:EPF_Lausanne07:41
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kanzureelectronic component/part selector/solver http://edasolver.com/07:51
ParahSailinyou dont use genetic engineering for bioremediation07:53
ParahSailingenerally you just give a carbon source or electron acceptor and one of the billions of species of bug in the dirt will take care of it07:54
ParahSailini feel like that igem team should have talked to at least one faculty member of an environmental engineering dept before wasting their time07:55
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ParahSailinor done a single lit search apparently http://link.springer.com/article/10.1007/s10532-008-9182-607:56
ParahSailinbut no, they have to try to make an effective metabolic pathway in a new bug by haphazardly sticking in transgenes07:57
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kanzurehttp://2014.igem.org/Team:BUGSS_Baltimore/Project "Baltimore Underground Science Space ... developing a new Biobrick for Pfu DNA polymerase, which offers a replication error rate approximately 6 fold lower than that of Taq polymerase... The team is now working to develop a kit for easy purification of Pfu polymerase with the goal of reducing the cost of this essential tool"08:33
kanzurewell this makes me feel pretty dumb:08:45
kanzurehttp://2014.igem.org/Team:Cooper_Union/TdT_project08:45
kanzurethey incorporated tdt into an alternative to phosphoramidite/oligonucleotide synthesis08:45
kanzureinstead of giving up when they couldn't electronically control tdt08:45
kanzureMinhaz Ud-Dean, S.M. (2008) A Theoretical Model for Template-Free Synthesis of Long DNA Sequence. Syst. Synth. Biol. 2:67-7308:48
kanzure"In the controllable system proposed by Ud-Dean, the reversibility of a 3' acetyl protective group was achieved by lowering pH during each cycle and thereby activating a deacetylase enzyme that is active at lower pH. During this step, TdT is also inactivated by the shift to lower pH, thereby preventing the addition of extra nucleotides. Our system simplifies this novel approach by using thermolabile reversible 3' protective groups. Since ...08:48
kanzure... our system uses heat to deprotect the dNTPs, only one step is needed instead of two, decreasing the time that is needed to add one base pair. This greatly increases the kinetics of the system since the time it takes to complete a full synthesis is equivalent to the time that it takes to complete one cycle multiplied by the number of base pairs that will be synthesized. "08:48
superkuhsci-hub's new wrapper proxy for IEEE stuff is great.08:50
superkuhWell, new to me at least.08:50
ParahSailinhm that sucks that TdT is thermolabile09:01
kanzurestrange that they didn't do any dna sequencing of their results09:06
kanzureor maybe they did and it doesn't work :)09:06
archelsany recommendations for 240VAC surge suppressors?09:11
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kanzure09:01 <+TallTed> the big perk from their IndieGoGo campaign is a trip to "see [their] particle accelerator in action"... why does a solar panel manufacturer need a particle accelerator? https://www.indiegogo.com/projects/rayton-solar-cheaper-than-fossil-fuels10:26
kanzurehaha genspace didn't listen to everyone complaining about DNA2.0's licensing policies on the diybio mailing list http://2014.igem.org/Team:Genspace/Project/IP-Free_Genes10:45
kanzurethat's what you get for isolationism i guess10:45
kanzure"we did not actually succeed in transferring the entire genome of Streptococcus thermophilus into Bacillus subtilis" http://2014.igem.org/Team:LA_Biohackers/Project11:08
kanzure"We currently have the methods to assemble large fragments of chemically synthesized DNA but no method for turning a piece of DNA into a functioning cell, aside from the method performed by the Venter Institute which only works on the smallest of bacterial chromosomes. With our strategy one could build the synthetic chromosome piecewise inside of Bacillus subtilis as part of the B subtilis chromosome. When the synthetic portion of the ...11:09
kanzure... chromosome is complete it is segregated from the B subtilis chromosome and is now contained within a functioning cytoplasm without the need for transferring it to a competent recipient cell. This would allow for the construction of large chromosomes using modular parts or chemically synthesized gBlocks or larger assemblies."11:09
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kanzuremicroglia ("mobile immune cells of the brain") conversion of human astrocytes into neurons, to remove astrogliosis build-up of glial scars caused by neural insults like brain injury, stroke and neurodegenerative disease http://2014.igem.org/Team:Lethbridge11:12
erasmusthat is why I'm growing my brainwith nsi11:12
kanzurefood allergen biosensor http://2014.igem.org/Team:Linkoping_Sweden11:14
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kanzurean expansion of the repertoire of ribosomes for the synthesis of proteins to select from hundreds of non-proteinogenic building blocks (rather than only amino acids) http://2014.igem.org/Team:Marburg:Project:NRPS11:25
kanzurethat seems like a great way to do directed evolution projects11:27
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eudoxiakanzure: have you had any new thoughts re:skdb since the last time we talked about it, when you said it took a wrong approach to hardware package management?11:32
kanzurei don't think i said that11:33
eudoxia2014-05-07.log:12:46 <kanzure> skdb is the wrong design, or at least, the wrong shape of the hypothetical solution11:34
kanzurei still agree that more cad would be useful11:34
kanzureand that comment was talking about project maintainers and incentives or something11:34
eudoxiayes, something about lacking incentives to write packages11:35
kanzurethe actual management of packages is a non-problem, in the sense that once you have them the workflows are quite similar to current software package maintenance workflows11:35
kanzureoctopart sort of has a lot of incentives to do packaging of electronics parts, but they don't do that11:37
kanzureecoli production of scFv antibodies http://2014.igem.org/Team:Michigan11:42
kanzuregeeze they really are worse than geocities http://2014.igem.org/Team:Missouri-Columbia/OurProject11:44
cluckjholy crap it just needs a flickering starscape background and it IS geocities11:47
eudoxiaholy shit11:47
yorickthat has to be on purpose11:52
yorickat least that's some skilled marquee usage11:53
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kanzureenzymatic conversion between human blood types http://2014.igem.org/Team:Tuebingen12:39
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kanzure"patentability index" http://2014.igem.org/wiki/images/8/84/AnnexIFinal.pdf 12:56
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poppingtonicwow, that page is just...wow. are those cells?13:15
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kanzuregenetically recoded organism (GRO)13:39
kanzurehaha i get it. instead of calling it a GMO.13:39
kanzurehttps://github.com/igemsoftware13:45
eudoxiaamazing, i found luke parrish on github trying some random usernames (docl)13:52
kanzureupdated http://diyhpl.us/wiki/dna/projects/ including the interesting projects from igem 201413:54
kanzureor at least, not including most of the not interesting projects13:54
kanzure.wik ribosome display14:09
yoleaux"Ribosome display is a technique used to perform in vitro protein evolution to create proteins that can bind to a desired ligand. The process results in translated proteins that are associated with their mRNA progenitor which is used, as a complex, to bind to an immobilized ligand in a selection step." — http://en.wikipedia.org/wiki/Ribosome_display14:09
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fenn"why does a solar panel manufacturer need a particle accelerator?" to embed dopant atoms below the surface of the silicon crystal17:02
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bbrittainI like GIO19:22
bbrittainGenetically Improved Organism19:23
bbrittainand you can just say guy-o19:23
superkuhscholar.google.com has effectively blocked the sci-hub proxy frame by incompatible captcha.19:23
superkuhOh, nevermind. Disabling JS fixes it.19:24
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kanzure"industrial" eeg http://www.biosemi.com/products.htm22:11
kanzure"It's rather curious the website says it's written in C against the libbitcoin library, as libbitcoin is a C++ library that doesn't even export C headers." brilliant22:12
kanzurealso: charcoal is a good answer, not lightning or wildfires22:52
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