| --- Log opened Fri May 11 00:00:07 2012 | ||
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| ThomasEgi | anyone knows a good resource about the anatomical details bout the ear and the nerves connecting to it | 04:51 |
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| chevbird | hey all! i'm relatively new here and would like to get a feel for the room. how many of you work in the biotech field vs how many of you are "amateurs" | 07:17 |
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| @kanzure | "Insufficient self-skepticism given how strong its claims are and how little support its claims have won. Rather than endorsing "Others have not accepted our arguments, so we will sharpen and/or reexamine our arguments," SI seems often to endorse something more like "Others have not accepted their arguments because they have inferior general rationality,"" | 09:00 |
| @kanzure | with apologies for linking to lesswrong.. | 09:00 |
| @kanzure | http://lesswrong.com/lw/cbs/thoughts_on_the_singularity_institute_si/ | 09:00 |
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| SDr | kanzure, that one is sooo full of win :D | 09:31 |
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| @kanzure | SDr: i don't understand why he wrote it.. givewell has 10's of thousands of orgs to monitor | 09:52 |
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| AlonzoTG | anyone know how to mount a shdc card in linux? | 10:05 |
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| chevbird | alonzotg: gui or command line | 10:21 |
| chevbird | also, what distro? a lot of package managers have the sdhc drivers in the community repos | 10:24 |
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| _0bitcount | I recently learned about "The Venus Project". Interesting development. Is anybody here acquainted with it? | 13:33 |
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| jrayhawk | AlonzoTG: typically 'mount /dev/mmcblk0p1 /path/to/mount/point', but dmesg and possibly ls -ltr /dev can tell you more | 13:40 |
| jrayhawk | you're probably best off asking these sorts of questions in distro-specific rooms. | 13:41 |
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| n_bentha | still no diybio news? | 15:05 |
| n_bentha | :( | 15:06 |
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| @kanzure | n_bentha: dyeh? | 15:09 |
| @kanzure | someone else should manually update that | 15:10 |
| yashgaroth | news update, some guy on biohack wants to do that telomerase virus thing on his 80 year old grandma | 15:10 |
| @kanzure | hahah | 15:11 |
| yashgaroth | he seems to be very gung ho about all the bio projects, despite not knowing any bio | 15:11 |
| @kanzure | why is he so focused on telomerase, again? | 15:12 |
| yashgaroth | because it's what all the people who have nearly no understanding of biology see as the holy grail | 15:14 |
| @kanzure | i blame the media | 15:14 |
| yashgaroth | oh totally, but I still like it as a good way to weed out such types | 15:14 |
| @kanzure | maybe he should sign his grandma up for cryonics or some good old fashion brain scanning | 15:15 |
| yashgaroth | oh good god "At first she said no, but then she said yes when I asked her again 10 minutes later. <Thank you early stage Alzheimers> " | 15:16 |
| @kanzure | actually, what's the cost for brain scanning at the moment? the material cost seems to be primarly preparing the brain tissue, slicing, then scanning and identifying neurons | 15:17 |
| @kanzure | *identifying features | 15:17 |
| yashgaroth | shouldn't need too much in the way of reagents, but it depends how accurate you plan to get | 15:19 |
| @kanzure | neat.. bosslab is raising a colony of photosynthetic sea slugs | 15:19 |
| @kanzure | yashgaroth: 3scan is presently identifying vascuoles and other properties of individual neurons | 15:20 |
| yashgaroth | well that shouldn't be too hard, vacuoles are bigger than a lot of the axons anyway | 15:20 |
| yashgaroth | ideally you'd have some way of mapping which receptors are at each junction | 15:21 |
| @kanzure | claiming 500nm resolution (apparently) | 15:21 |
| @kanzure | individual receptor resolution sounds much harder (without tagging) | 15:22 |
| @kanzure | i'm familiar with one or two ways to tag receptors and ion channels if you are doing genetic engineering | 15:22 |
| @kanzure | not sure about after-the-fact tagging.. antibody tagging? | 15:22 |
| yashgaroth | yeah that would be easier, at least for human brains | 15:22 |
| yashgaroth | with a transgenic mouse, you could make fusions to a variety of fluorescent proteins, but they'd probably be very stupid mice | 15:23 |
| @kanzure | yashgaroth: did you see my ranting about nootropic simulations the other day, and if so, do you have a better scheme? | 15:25 |
| yashgaroth | mmm lemme read it real quick | 15:26 |
| @kanzure | david pearce ranting about biohacking http://ieet.org/index.php/IEET/more/pearce20120510 | 15:26 |
| @kanzure | http://www.biointelligence-explosion.com/ | 15:26 |
| @kanzure | his excuse for friendliness is telepathy? what | 15:28 |
| yashgaroth | well most noots will work by modifying how often a certain (type of) receptor will activate a junction, but I'll need to see how much functionality this neuron program has | 15:28 |
| @kanzure | yashgaroth: http://gnusha.org/logs/2012-05-07.log | 15:29 |
| yashgaroth | if you have the supercomputer to run a brain simulation, might as well try protein receptor simulation to find a noot that binds more effectively | 15:31 |
| @kanzure | yashgaroth: yes but how do you extrapolate from "this receptor acting differently" to specific performance results? | 15:34 |
| @kanzure | at the moment i think "taking graphs/charts from the old literature about modulated receptor activity" would be sufficient (but protein/receptor simulations would be ideal) | 15:35 |
| yashgaroth | I'd imagine almost all noots will make a corresponding type of neuron more likely to fire | 15:35 |
| @kanzure | gaahhh | 15:35 |
| @kanzure | nope. | 15:35 |
| @kanzure | some neurons are inhibitory and some are excitatory | 15:35 |
| @kanzure | some have different firing patterns | 15:35 |
| yashgaroth | sure, but most of the useful ones will be stimulants | 15:36 |
| @kanzure | stimulants don't actually increase firing rates | 15:36 |
| @kanzure | when you look under fmri at stimulated cortices you see /less/ firing | 15:36 |
| yashgaroth | well shit | 15:37 |
| @kanzure | yes :| | 15:37 |
| @kanzure | there are many other non-obvious ways you can imagine the brain operating | 15:37 |
| @kanzure | for instance! certain pathways between different neuroanatomical regions have different operating characteristics | 15:37 |
| @kanzure | GABA inhibitory pathways to the thalamus for instance are somewhat responsible for sensory information (gah don't quote me) | 15:37 |
| @kanzure | superkuh: do you have a good or favorite example for specific pathways that a nootropic impacts in some positive way? | 15:38 |
| yashgaroth | it does make sense, since a molecule binding is far more likely to block function of a protein than to activate it more | 15:40 |
| @kanzure | yashgaroth: http://superkuh.com/library/Neuroscience/Thalamus/Gating%20in%20Cerebral%20Networks_%20Mircea%20Steriade_%20Denis%20Pare_%202007.pdf | 15:40 |
| @kanzure | look at chapter 5 i guess.. i am not happy with this example tho | 15:40 |
| @kanzure | (page 99) | 15:42 |
| yashgaroth | ah thank you they don't list the chapter on the pages for some reason | 15:42 |
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| @kanzure | page 2 has an interesting circuitry diagram | 15:44 |
| @kanzure | http://superkuh.com/library/Neuroscience/Large-scale%20model%20of%20mammalian%20thalamocortical%20systems_%20Eugene%20M%20Izhikevich_%20Gerald%20M%20Edelman_%202011_%20PNAS-2008-Izhikevich-3593-8.pdf | 15:44 |
| @kanzure | or page s3 | 15:44 |
| @kanzure | heh they do fMRI simulations from their models, that has to be fun | 15:46 |
| yashgaroth | neuro is on my list to learn, but it's below biochem and immuno | 15:47 |
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| Juul | I was just at DNA 2.0 | 16:17 |
| Juul | Notes: They don't use Tecan liquid handling robots, even though they like them better, because they cannot replace the software with their own and integrate into their pipeline. They use Biolytic Dr. Oliog 192 machines that do 2 x 96 well plates at a time, 5-6 hours for a run, 50-100 nt oligo per well | 16:17 |
| AdrianG | do SSRIs impact opioid pathways | 16:17 |
| AdrianG | or not | 16:17 |
| Juul | They use an old-school Applied Biosystems 3948 Nucleic Acid Synthesis machine (not sold anymore, bought on ebay) to do difficult / different oligos that require tweaking of the chemistry/timing/conditions because it is easier to tweak (more macroscopic and simpler than the Dr. Oligo) | 16:17 |
| @kanzure | yeah, i think the entire dna synthesis market is served by refurbished ABI equipment :/ | 16:17 |
| Juul | For sequencing they use an AB 3730XL DNA Analyzer | 16:17 |
| Juul | hah | 16:18 |
| Juul | I was surprised to see a portion of the lab dedicated to casting and running gels | 16:19 |
| Juul | some of the stuff they do apparently requires gel separation | 16:19 |
| yashgaroth | one would hope so | 16:20 |
| Juul | how so? | 16:20 |
| yashgaroth | to separate out sequences of the correct length | 16:20 |
| Juul | I'm not sure how they eliminate the incorrect sequences. Maybe I wasn't paying enough attention, but I'm pretty sure they don't run everything on a gel, only some things. | 16:23 |
| Juul | maybe PCR is enough | 16:23 |
| Juul | to get high enough purity | 16:23 |
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| yashgaroth | depends on how long the oligo is | 16:24 |
| yashgaroth | especially for assembling multiples, you'd need to separate them on a gel | 16:24 |
| Juul | assembling multiples? | 16:24 |
| yashgaroth | overlap extension PCR | 16:25 |
| skorket | Do you think there is a market for a low cost pcr machine? | 16:25 |
| Juul | yashgaroth, you're saying you'd need to separate all of the non-assembled or partially assembled DNA from the full assembly? | 16:26 |
| yashgaroth | why not | 16:26 |
| yashgaroth | yes | 16:26 |
| yashgaroth | normally you wouldn't do it for short oligos I guess, but it depends what kind of quality the client wants | 16:27 |
| Juul | don't you think that amplifying the whole assembly a final PCR after assembly would be enough for most? | 16:28 |
| Juul | assembly _with_ a final PCR | 16:28 |
| Juul | hrm, why is the openPCR so expensive | 16:28 |
| yashgaroth | sure, but they'll still need to run a gel at some point | 16:29 |
| yashgaroth | takes less time than sequencing | 16:29 |
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| Juul | hm | 16:30 |
| Juul | it seems so primitive | 16:30 |
| Juul | especially given the lack of automation | 16:30 |
| Juul | all the gels were hand-cast | 16:30 |
| yashgaroth | true, you'd think with high-throughput they'd use a microfluidics system, so it implies they're cutting out bands on the gel | 16:30 |
| @kanzure | i think they sequence and then throw any errors out | 16:31 |
| Juul | they do sequence everything | 16:31 |
| Juul | i'll get to ask them more questions in a few weeks | 16:31 |
| @kanzure | skorket: openpcr.com is pretty expensive, there were a few thousand people who bought them though.. there's currently a $50k backlog of unshipped openpcr units | 16:31 |
| @kanzure | skorket: i think there's a lot of opportunity for a <$100 pcr device | 16:31 |
| @kanzure | yashgaroth: yeah, i definitely expect them to be cutting out gel slices by hand (unless they are automating it, which, it turns out, they are not) | 16:32 |
| Juul | I asked one of the founders about their strategy for the future, given that we can probably expect the next generation of synthesis to at least 10 times cheaper and faster, possibly much more than that | 16:32 |
| @kanzure | there's actually no widely publicized "next generation synthesis" | 16:33 |
| Juul | he started talking about how t-shirt companies have to deal with new t-shirts coming out, and said it had been working ok for the past almost 10 years, and i said "so far so good?" and he said "so far so good' | 16:33 |
| Juul | not yet, but i find it unlikely that there won't be a next generation synthesis within the next 10 years | 16:34 |
| skorket | you think $150-250 is too much? | 16:34 |
| yashgaroth | the price is dropping a lot slower than sequencing, and dna2.0 does have their "proprietary codon optimization" bullshit to ride on | 16:34 |
| @kanzure | Juul: obv. he wouldn't tell you the actual strategy they have ;) | 16:35 |
| @kanzure | skorket: i dont think it's too much.. i just think it's not the cheapest it can be | 16:35 |
| skorket | When you're talking low production at consumer prices: $10 power supply, $10 peltier, $10 misc electronics, $10 aluminum block, $10 casing, $10 misc. | 16:36 |
| Juul | kanzure, yes, and the obvious reason that comes to mind is that he's planning to dump the company, otherwise he would be talking about his proprietary codon optimization and all of the design-level expertise. they're also spinning up a partner company that specializes in machine learning applied to pathway design as a service | 16:36 |
| skorket | If I wanted to make one myself, no question I could do it for < $100 | 16:36 |
| skorket | but selling it's another matter | 16:36 |
| @kanzure | Juul: pathway design as a service sounds fun, but debugging it is a pain in the butt? | 16:37 |
| @kanzure | Juul: i mean.. damn, you have to do some directed evolution sometimes to get a pathway to do what you want, unless it's a simple plug-and-chug thing | 16:37 |
| @kanzure | and even then it might not be optimized to actually work or do whatever it is you want | 16:37 |
| Juul | kanzure, yeah i'm not sure how the debugging is going to work, it seems they're only just started this up and it's still just happening as part of DNA 2.0 | 16:37 |
| delinquentme | Juul, you're talking about this >> http://genomecompiler.com/ | 16:37 |
| @kanzure | no he's not | 16:38 |
| Juul | no | 16:38 |
| @kanzure | genomecompiler.com is just some software crap | 16:38 |
| delinquentme | what pathways? | 16:38 |
| @kanzure | it's an IDE or something.. pass | 16:38 |
| @kanzure | delinquentme: the ones the customers want | 16:38 |
| delinquentme | kanzure, *eye roll* | 16:38 |
| Juul | it's CAD software for DNA design | 16:38 |
| @kanzure | skorket: perhaps not the most useful version.. http://russelldurrett.com/lightbulbpcr.html | 16:38 |
| @kanzure | Juul: there's all sorts of products that claim to do that | 16:39 |
| Juul | yep | 16:39 |
| @kanzure | and each year at igem there's even more. "clotho" used to be the big thing. ugh. | 16:39 |
| Juul | Cesar, the guy who was working for the BIOFAB, is now at genome compiler | 16:39 |
| @kanzure | Juul: the reality is that synthetic biology is not at that level yet, and their press releases are sorta lying about it | 16:39 |
| skorket | kanzure, Yeah, I've seen that before. I actually think that's pretty clever. In the end, it's just about making it convenient really | 16:39 |
| @kanzure | skorket: there was a ton of talk on the diybio mailing list about thermocycler design | 16:40 |
| @kanzure | skorket: most of the original openpcr design decisions were made in that thread | 16:40 |
| @kanzure | but there were also people suggesting cheaper alternatives | 16:40 |
| @kanzure | i suggest you look at it? | 16:40 |
| @kanzure | oh also there was shit on openwetware.. http://openwetware.org/wiki/DIYbio:Notebook/Open_Thermal_Cycler | 16:40 |
| Juul | kanzure, hm yeah, but I do think we can have better software tools than what people are generally using right now | 16:40 |
| @kanzure | mailing list discussion: https://groups.google.com/forum/?fromgroups#!topic/diybio/8oMYA5LxbN0 | 16:41 |
| @kanzure | Juul: for sure | 16:41 |
| Juul | BIOFAB was a bunch of google docs, excel sheets and a bit of APE for most of the work | 16:41 |
| @kanzure | Juul: i'm pretty sure you're a better programmer than that. what gives? | 16:41 |
| Juul | kanzure, i wasn't there at the beginning | 16:41 |
| @kanzure | Juul: so regarding dna 2.0.. you said they only had one synthesizer and one sequencer? | 16:42 |
| @kanzure | oh wait, i didn't fully read the line about tecan either... they know about jonathan cline's perl module for running tecan equipment, right? | 16:42 |
| Juul | kanzure, ah no, i'm not sure how many sequencers they have, I saw four Dr. Oligo machines, and at two ABI machines. I'm not sure how many they have total. | 16:43 |
| @kanzure | it's up on cpan under Robotics::Tecan or something | 16:43 |
| skorket | http://heybryan.org/~bbishop/docs/protocols/pcr.xml <-- dead link | 16:43 |
| @kanzure | skorket: yeah, sorry, totally my fault.. oen sec | 16:43 |
| Juul | kanzure, not sure, i'll mention it to them. | 16:43 |
| @kanzure | Juul: if they would be interested in paying for work to be done on that, jonathan would probably be up for it | 16:44 |
| @kanzure | skorket: http://diyhpl.us/~bryan/irc/pcr.xml | 16:44 |
| delinquentme | alright TTYL all im going to be korean for a bit | 16:45 |
| delinquentme | >_<;;;;;;;; | 16:45 |
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| @kanzure | skorket: that was part of a broader discussion about how to automate protocols | 16:45 |
| skorket | yep, just seemed relevant. Thanks for making it available | 16:46 |
| @kanzure | it was already there.. i just suck at keeping old broken links redirecting to where the new content is | 16:46 |
| @kanzure | *new location is | 16:46 |
| @kanzure | skorket: regarding protocol automation.. http://gnusha.org/logs/2012-04-08.log see the links to 88proof | 16:47 |
| @kanzure | 88proof is jonathan cline's blog (who we were just talking about because he wrote the perl modules to interface/control tecan liquid handling machines) | 16:47 |
| @kanzure | oh oops. wrong gnusha.org log link.. that was just about microfluidics, not protocols. one sec. | 16:47 |
| skorket | I see diginet talking about the outrageous price of OpenPCR | 16:48 |
| @kanzure | i meant to link to this one - http://gnusha.org/logs/2012-03-15.log which has the discussion about protocol representation | 16:48 |
| @kanzure | this should probably be added to the wiki, dunno why i'm linking to logs that link to logs | 16:48 |
| skorket | When designing this type of thing, where do you want the temperature sensor? | 16:49 |
| @kanzure | the more temperature sensors the better! :P | 16:49 |
| @kanzure | i want one closest to the heat generator and one that is farthest away, at minimum | 16:49 |
| @kanzure | for water baths i think some people just use a submersible sensor and move on? | 16:50 |
| @kanzure | Juul: the exact link is http://search.cpan.org/~jcline/Robotics-0.21/lib/Robotics/Tecan.pm | 16:50 |
| skorket | So, ideally, at a minimum, you would want a sensor underneath, on the top and another where you could submerge it in water? | 16:51 |
| skorket | in a dummy position, say? | 16:51 |
| @kanzure | Juul: he seemed to be using sourceforge :( https://jcline.svn.sourceforge.net/svnroot/jcline/laboratory-robots-tecan/ | 16:51 |
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| @kanzure | skorket: i think in a cheap thermocycler you would probably not be using water baths | 16:51 |
| @kanzure | skorket: it's up to you of course | 16:52 |
| skorket | just trying to get a sense | 16:52 |
| @kanzure | i can't answer your exact question, sorry. i don't know if there should be a sensor near each micropipette tube or not. i'm pretty sure there usually aren't because that would dramatically increase the number of sensors in standard thermocyclers (especially the X-by-Y pcr arraying machines) | 16:53 |
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| skorket | I'll just have to play around with it. I wish there was a source of really cheap temperature sensors so I could blanket the thing | 16:57 |
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| @kanzure | Juul: when you have a moment, could you look over my ranting about how to do nootropic simulation? http://gnusha.org/logs/2012-05-07.log perhaps you have a better idea | 16:57 |
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| AdrianG | why is chemistry so stupid | 16:58 |
| AdrianG | nothing is rigorous in chemistry | 16:58 |
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| fenn | did someone say photosynthetic sea slugs? http://fennetic.net/irc/IMG_6609.JPG | 18:31 |
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| @kanzure | fenn: do you keep some? | 18:52 |
| fenn | not yet | 19:01 |
| fenn | the picture is from an aquatic petting zoo in santa cruz | 19:02 |
| fenn | i have an aquarium sitting around waiting for me to put some effort into it | 19:02 |
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| nmz787_ | How do i search all the logs easily? | 20:22 |
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| yashgaroth | google search with inurl:gnusha.org/logs added? | 20:25 |
| nmz787_ | Im trying to find a hobby cnc mill i mentioned earlier | 20:25 |
| nmz787_ | Is inurl different than site: ? | 20:27 |
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| yashgaroth | probably | 20:27 |
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| @kanzure | nmz787_: you can download the logs and do grep | 20:33 |
| @kanzure | nmz787_: do you mean the quantum fireball thing | 20:35 |
| nmz787_ | Yeah, found it | 20:36 |
| nmz787_ | Sending to roommate | 20:36 |
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| JayDugger | Good evening, everyone. | 20:56 |
| @kanzure | so why haven't we extracted dinosaur dna yet? | 21:06 |
| yashgaroth | not much left to extract | 21:07 |
| @kanzure | yashgaroth: i'm pretty sure we've found old fossilized tissue somewhere? | 21:07 |
| yashgaroth | sure, but 65 million years can be hard on DNA, stable as it is | 21:08 |
| yashgaroth | and if you've got a bunch of 10 bp fragments, they're impossible to assemble | 21:08 |
| @kanzure | hrm http://en.wikipedia.org/wiki/Ancient_DNA | 21:09 |
| @kanzure | "Current estimates suggest that in optimal environments, i.e. environments which are very cold, such as permafrost or ice, an upper limit of around 1 million years exi" | 21:09 |
| yashgaroth | sounds about right | 21:09 |
| @kanzure | i'd like to see those estimates | 21:10 |
| yashgaroth | hahaha "The Dinosaur DNA was later revealed to be human Y-Chromosome" | 21:11 |
| yashgaroth | well, one can only extrapolate the rate of degradation at higher temperatures compared to frozen, unless someone did a 10-year -80C experiment and went from that | 21:12 |
| @kanzure | no i mean an "anders sandberg" "intelligent superobjects" style analysis of the limits of ancient dna | 21:12 |
| yashgaroth | you lost me at whatever that is | 21:13 |
| @kanzure | analyses like this: | 21:14 |
| @kanzure | http://www.orionsarm.com/fm_store/Brains2.pdf | 21:14 |
| @kanzure | jeeze is orionsarm.com the only place with a backup of this? | 21:14 |
| yashgaroth | to the serveratory! | 21:15 |
| @kanzure | another popular example of this type of "theoretical limits" paper is "Search for Artificial Stellar Sources of Infra-Red Radiation" (that dyson paper about dyson spheres) | 21:16 |
| @kanzure | anyway, i haven't found one of these for the physics of extremely ancient dna | 21:17 |
| yashgaroth | math and DNA don't mix | 21:17 |
| nmz787__ | Kanzure, so whats your ability to move if i move out there? | 21:19 |
| nmz787__ | Still have will? | 21:19 |
| @kanzure | nmz787__: eh, it's slightly more annoying since i signed a lease agreement, but i can get out of it | 21:20 |
| nmz787__ | Also me working with sequencers in nyc could have its benefits | 21:20 |
| nmz787__ | If i get the cornell gg | 21:20 |
| nmz787__ | Gg | 21:20 |
| nmz787__ | Gig | 21:20 |
| @kanzure | nmz787__: why should i move? i have comparatively cheap housing | 21:21 |
| nmz787__ | Well we're looking into 2brdroom if you want to come stay and collaborate in nyc on synthesis ... | 21:22 |
| nmz787__ | For abweek or two here and there | 21:22 |
| @kanzure | nyc is super expensive. i guess i'm already paying nyc income tax a few times over, so maybe it makes sense.. | 21:23 |
| @kanzure | yashgaroth: what about ancient viruses. those should be relatively well protected in fossils? | 21:24 |
| nmz787__ | we're looking at $1750 for 2bdroom loft wih garage in brooklyn ~25 mins from genspace, and 15 from Manhattan | 21:24 |
| yashgaroth | not sufficiently more so than living DNA | 21:25 |
| @kanzure | not bad | 21:25 |
| @kanzure | "A Proteomics Jurassic Park: The isolation of proteins from microorganisms encapsulated in amber from the Oligo-Miocene epoch 30-40 million years ago" | 21:25 |
| @kanzure | meh proteins | 21:26 |
| @kanzure | why wouldn't dna survive in amber? | 21:26 |
| nmz787__ | Nuclease ribozymes | 21:26 |
| yashgaroth | it'd survive better than protein | 21:27 |
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| @kanzure | yashgaroth: from what i can tell.. it seems to be mostly one or two reports popping up where some group claims to have extracted dna using some really lousy methods, | 21:33 |
| @kanzure | and a second professor shows up and questions their methods | 21:33 |
| @kanzure | there doesn't seem to be any critical overview of techniques or methods for this extraction (even in principle) | 21:34 |
| yashgaroth | to be fair they do have a reference to Jurassic Park in the paper, which I doubt is peer reviewed | 21:34 |
| @kanzure | for instance, i would expect to see at least one paper outlining the possible scenarios leading to well-preserved ancient dna (assuming the theoretical physics works out) | 21:34 |
| @kanzure | "Problems of reproducibility - does geologically ancient DNA survive in amber-preserved insects?" | 21:35 |
| @kanzure | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1688388/pdf/9149422.pdf | 21:35 |
| @kanzure | like.. why would you use pcr if you haven't identified a single dna molecule yet? | 21:39 |
| yashgaroth | what other methods could you use? except possibly nanopores, which came about after this paper | 21:40 |
| @kanzure | you can identify single molecules of dna through atomic force microscopy | 21:41 |
| @kanzure | once you have identified a single strand of dna you can then consider using pcr or something | 21:41 |
| yashgaroth | I don't think they could read DNA with EM back then | 21:42 |
| @kanzure | sure, but you can still see it | 21:42 |
| yashgaroth | either way you'd just need to throw in a library of primers and see what sticks | 21:42 |
| @kanzure | what the hell primers did they choose to use for pcr?? | 21:42 |
| yashgaroth | all of them, basically | 21:43 |
| @kanzure | "We have used a range of PCR conditions and primers" | 21:43 |
| @kanzure | i suppose it's safe to assume that some of the primers should work on an in-tact ancient genome, but uh if you're arguing only fragments survive in the first place.. | 21:44 |
| yashgaroth | you don't need a long fragment to get a read, I suppose | 21:44 |
| @kanzure | so it looks like the current upper limit (according to that paper) is 100,000 years | 21:45 |
| yashgaroth | there were some reports about germinating seeds from permafrost that were a few thousands years old | 21:46 |
| yashgaroth | of years* | 21:46 |
| @kanzure | my other complaint is that these guys trying to do pcr amplification from bugs-in-amber seem to be just trying random techniques to amplify dna, rather than physically finding the dna first.. bleh | 21:47 |
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| yashgaroth | at that point you can only assume there's DNA, EM detection of it is almost impossible outside of tightly controlled setups | 21:49 |
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| @kanzure | "Non-destructive sampling of ancient insect DNA" neat | 21:50 |
| @kanzure | "A statistical approach to identify ancient template DNA" | 21:50 |
| @kanzure | "Evaluating the Impact of Post-Mortem Damage in Ancient DNA: A Theoretical Approach" but 2011? bleh | 21:52 |
| yashgaroth | I'd say it's at best 50/50 that even a god could assemble a dinosaur genome | 21:53 |
| @kanzure | "Assuming physiological salt concentrations, neutral pH and a temperature of 15 C, it would take about 100k years for hydrolytic damage to destroy all DNA that could be reasonably retrieved (Hoxreiter et al., 2001)." | 21:56 |
| @kanzure | *Hofreiter | 21:57 |
| @kanzure | that ref is http://email.eva.mpg.de/~paabo/pdf1/HofreiterAncDNA_NatRev2001.pdf | 21:57 |
| @kanzure | oh god the typesetting | 21:58 |
| @kanzure | blah he just uses another reference.. "Instability and decay of the primary structure of DNA" | 22:01 |
| yashgaroth | still not open access after 20 years it seems | 22:01 |
| yashgaroth | 100k years seems like a high estimate, since it would imply frozen DNA would last at lot longer | 22:03 |
| @kanzure | this seems all sorts of absurd- haven't the panspermia people figured DNA would last longer than a few million years on asteroids ? | 22:04 |
| yashgaroth | 'figured' and 'proven' are quite different | 22:04 |
| @kanzure | "Studies of bacteria frozen in Antarctic glaciers have shown that DNA has a half-life of 1.1 million years under such conditions, suggesting that while life may have potentially moved around within the Solar System it is unlikely that it could have arrived from an interstellar source. [68]" | 22:06 |
| @kanzure | [68] is http://ur.rutgers.edu/medrel/viewArticle.html?ArticleID=5898 | 22:06 |
| @kanzure | "DB error 3" hooray | 22:06 |
| yashgaroth | the idea of a half-life of DNA is wildly unspecific | 22:07 |
| @kanzure | and hilarious | 22:07 |
| yashgaroth | it's compounded by the appeal of the field of extraterrestrial life being attractive to nutjobs | 22:10 |
| yashgaroth | ...which happens, to a lesser extent, with life-extension research sadly | 22:10 |
| yashgaroth | on an unrelated note, another person on biohack has volunteered a grandparent | 22:11 |
| @kanzure | yashgaroth: there's a very fine line between "diy transhumanism" and "snake oil" | 22:12 |
| yashgaroth | the DIY aspect hasn't been as corrupted yet, but my god the amount of utterly insane shit within the umbrella of transhuman is just horrifying | 22:12 |
| yashgaroth | when "I just want to become the galaxy-sized octoflyrhino I've always wanted to be" is considered practically normal | 22:14 |
| @kanzure | feel free to make up a specific outline of boundaries | 22:15 |
| @kanzure | like on the one hand there's this: | 22:15 |
| yashgaroth | I'd have no idea where to begin | 22:15 |
| @kanzure | http://www.maxmore.com/extprn3.htm | 22:15 |
| * strangewarp notes at this point that some people want very weird bodmods and aren't insane | 22:15 | |
| @kanzure | strangewarp: furries are sorta crazy, sorry | 22:16 |
| @kanzure | i haven't seen a realistic roadmap from a furry yet | 22:16 |
| yashgaroth | as a representative of the SA forums, I'll stay out of this discussion | 22:16 |
| strangewarp | kanzure: Sadly, they are, which is why you don't see very any of them pursuing transhumanism and why you see a /ton/ of them doing silly totemic shit | 22:16 |
| strangewarp | very many* | 22:16 |
| @kanzure | yashgaroth: i have also been conditioned to have a very strong anti-furry bias, but hopefully it doesn't show | 22:17 |
| @kanzure | yashgaroth: anyway! so we have stuff like http://www.maxmore.com/extprn3.htm | 22:17 |
| @kanzure | yashgaroth: but in the mean time we have things like "LOL ADENOVIRUSES FOR G-MA, THE BIG G" | 22:17 |
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| yashgaroth | on the one hand, it could be said they're actually (planning to) do stuff, but it's still like lepht, not giving a good face to the movement | 22:19 |
| @kanzure | you know, now that i look at it, | 22:19 |
| @kanzure | those principles don't list anything about studying current technology | 22:19 |
| @kanzure | "Applying science and technology creatively to transcend "natural" limits imposed by our biological heritage" is sorta close, but people take "creatively" to mean "LOL IDEAS CAN MEAN WHATEVER I WANT" | 22:19 |
| strangewarp | frigging Lepht... I once saw a room full of furries gush about how "awesome" she is. Blurgh | 22:19 |
| yashgaroth | mental masturbation about dyson spheres etc isn't any better | 22:20 |
| yashgaroth | I'm just trying to find the thin line in between, if it exists | 22:20 |
| @kanzure | i think theoretical studies of dyson spheres are interesting, but i haven't seen a reasonable plan for construction yet, and i think the "plans for detection" are already implemented | 22:20 |
| yashgaroth | oh, detection is a different story | 22:21 |
| yashgaroth | but why bother figuring out whether a sphere or ring is better for making one | 22:21 |
| yashgaroth | rather than working on quantum computing or anything actually relevant to the next thousand years | 22:22 |
| @kanzure | there are a few silos of "advanced" transhumanist work- like in cryonics; SENS' (ex) molecular biologists; some neural computing groups; etc. | 22:24 |
| @kanzure | but largely, most transhumanists are relatively unskilled in modern technology | 22:24 |
| yashgaroth | unnamed people writing treatises on uplifting animals and shit like that is such a colossal waste that I can't comprehend it | 22:24 |
| @kanzure | yashgaroth: brain scanning animals is a useful case for figuring out how to scan a human brain properly | 22:24 |
| @kanzure | for instance, davidad is working on worm neuron emulation | 22:24 |
| yashgaroth | yes, but that's actually relevant | 22:25 |
| yashgaroth | figuring out the best way to make dolphins able to talk about fish is...less so | 22:26 |
| @kanzure | yashgaroth: the problem is that many people dismiss the "you need to study molecular biology for X years" as pessimism | 22:27 |
| @kanzure | it's not pessimism, it's good advice | 22:27 |
| yashgaroth | I'm not suggesting anything outside of STEM is a waste of brainpower, per se | 22:28 |
| @kanzure | sure.. i'm just talking about the limited case of "a very high level of crazies in the transhumanist community that can't seem to get the technology straight" | 22:29 |
| @kanzure | wherein people take "the future, mannn" and extrapolate it to mean "anything" | 22:29 |
| yashgaroth | to be fair, we haven't given them a whole lot of concrete stuff to work with yet | 22:29 |
| strangewarp | Rational topology is required, and that's something few people realize | 22:30 |
| yashgaroth | I'm also pissed off because all these fucking kurzweil AI types dismiss biology immediately, because in 200 years AI will run everything so why even bother | 22:31 |
| @kanzure | yashgaroth: electronics, software, some basic molecular biology, wearable computing, there's lots of accessible vaguely transhumanist stuff | 22:31 |
| yashgaroth | it's still vague though...if we consider google glasses to be transhuman, so are wristwatches | 22:32 |
| @kanzure | well, when someone brings up the "where's the cutoff" argument, i resort to talking about "transhuman technologies are primarily those that increase your ability to enhance yourself" | 22:32 |
| @kanzure | so, "the minimal viable nootropic" is the nootropic that lets you build an even more powerful nootropic | 22:33 |
| @kanzure | *minimally viable? | 22:33 |
| @kanzure | grammar! | 22:33 |
| strangewarp | Oh, that's a clever definition, I'll have to remember it | 22:33 |
| yashgaroth | wristwatches get you to transhumanist meetups on time :P | 22:33 |
| @kanzure | yashgaroth: dude my wristwatch *is* my presentation. look at it! it's so shiny. it beeps! and it runs java. | 22:33 |
| yashgaroth | ah, but is it embedded into your skin for no reason? | 22:34 |
| @kanzure | because the first thing i think when seeing a wristwatcch is, "ah, but does it run java" >_< | 22:34 |
| @kanzure | *wristwatch | 22:34 |
| * yashgaroth goes to scavenge for food | 22:38 | |
| skorket | hey, just to chime in, I take a lot of what Kurzweil says about AI but I think biology is going to be critical in the next couple of decades. I believe biotech is going to be the next computer revolution, except bigger | 22:40 |
| skorket | one doesn't need to be sacrificed for the other | 22:41 |
| yashgaroth | one can only hope | 22:56 |
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| -!- Mokbortolan_1 [~Nate@c-76-115-136-13.hsd1.or.comcast.net] has quit [Ping timeout: 244 seconds] | 23:21 | |
| -!- strages_1hop [~strages@256.makerslocal.org] has quit [Ping timeout: 256 seconds] | 23:25 | |
| --- Log closed Sat May 12 00:00:08 2012 | ||
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