--- Log opened Fri May 11 00:00:07 2012
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04:51 < ThomasEgi> anyone knows a good resource about the anatomical details bout the ear and the nerves connecting to it
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07:17 < 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"
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09:00 <@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/
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09:31 < SDr> kanzure, that one is sooo full of win :D
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09:52 <@kanzure> SDr: i don't understand why he wrote it.. givewell has 10's of thousands of orgs to monitor
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10:05 < AlonzoTG> anyone know how to mount a shdc card in linux?
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10:21 < chevbird> alonzotg: gui or command line
10:24 < chevbird> also, what distro?  a lot of package managers have the sdhc drivers in the community repos
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13:33 < _0bitcount> I recently learned about "The Venus Project". Interesting development. Is anybody here acquainted with it?
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13:40 < jrayhawk> AlonzoTG: typically 'mount /dev/mmcblk0p1 /path/to/mount/point', but dmesg and possibly ls -ltr /dev can tell you more
13:41 < jrayhawk> you're probably best off asking these sorts of questions in distro-specific rooms.
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15:05 < n_bentha> still no diybio news?
15:06 < n_bentha> :(
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15:09 <@kanzure> n_bentha: dyeh?
15:10 <@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
15:11 <@kanzure> hahah
15:11 < yashgaroth> he seems to be very gung ho about all the bio projects, despite not knowing any bio
15:12 <@kanzure> why is he so focused on telomerase, again?
15:14 < 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
15:15 <@kanzure> maybe he should sign his grandma up for cryonics or some good old fashion brain scanning
15:16 < 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> "
15:17 <@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
15:19 < 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
15:20 <@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
15:21 < yashgaroth> ideally you'd have some way of mapping which receptors are at each junction
15:21 <@kanzure> claiming 500nm resolution (apparently)
15:22 <@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
15:23 < yashgaroth> with a transgenic mouse, you could make fusions to a variety of fluorescent proteins, but they'd probably be very stupid mice
15:25 <@kanzure> yashgaroth: did you see my ranting about nootropic simulations the other day, and if so, do you have a better scheme?
15:26 < 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/
15:28 <@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
15:29 <@kanzure> yashgaroth: http://gnusha.org/logs/2012-05-07.log
15:31 < 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
15:34 <@kanzure> yashgaroth: yes but how do you extrapolate from "this receptor acting differently" to specific performance results?
15:35 <@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
15:36 < 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
15:37 < 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)
15:38 <@kanzure> superkuh: do you have a good or favorite example for specific pathways that a nootropic impacts in some positive way?
15:40 < 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
15:42 <@kanzure> (page 99)
15:42 < yashgaroth> ah thank you they don't list the chapter on the pages for some reason
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15:44 <@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
15:46 <@kanzure> heh they do fMRI simulations from their models, that has to be fun
15:47 < yashgaroth> neuro is on my list to learn, but it's below biochem and immuno
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16:17 < 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
16:18 < Juul> hah
16:19 < 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
16:20 < yashgaroth> one would hope so
16:20 < Juul> how so?
16:20 < yashgaroth> to separate out sequences of the correct length
16:23 < 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
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16:24 < 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?
16:25 < yashgaroth> overlap extension PCR
16:25 < skorket> Do you think there is a market for a low cost pcr machine?
16:26 < 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
16:27 < yashgaroth> normally you wouldn't do it for short oligos I guess, but it depends what kind of quality the client wants
16:28 < 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
16:29 < yashgaroth> sure, but they'll still need to run a gel at some point
16:29 < yashgaroth> takes less time than sequencing
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16:30 < 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
16:31 <@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
16:32 <@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
16:33 <@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'
16:34 < 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
16:35 <@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
16:36 < 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
16:37 <@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/
16:38 <@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
16:39 <@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
16:40 <@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
16:41 <@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
16:42 <@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?
16:43 < 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.
16:44 <@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
16:45 < delinquentme> alright TTYL all im going to be korean for a bit
16:45 < delinquentme> >_<;;;;;;;;
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16:45 <@kanzure> skorket: that was part of a broader discussion about how to automate protocols
16:46 < 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
16:47 <@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.
16:48 < 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
16:49 < 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
16:50 <@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
16:51 < 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/
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16:51 <@kanzure> skorket: i think in a cheap thermocycler you would probably not be using water baths
16:52 <@kanzure> skorket: it's up to you of course
16:52 < skorket> just trying to get a sense
16:53 <@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)
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16:57 < 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
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16:57 <@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
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16:58 < AdrianG> why is chemistry so stupid
16:58 < AdrianG> nothing is rigorous in chemistry
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18:31 < fenn> did someone say photosynthetic sea slugs? http://fennetic.net/irc/IMG_6609.JPG
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18:52 <@kanzure> fenn: do you keep some?
19:01 < fenn> not yet
19:02 < 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
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20:22 < nmz787_> How do i search all the logs easily?
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20:25 < yashgaroth> google search with inurl:gnusha.org/logs added?
20:25 < nmz787_> Im trying to find a hobby cnc mill i mentioned earlier
20:27 < nmz787_> Is inurl different than site: ?
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20:27 < yashgaroth> probably
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20:33 <@kanzure> nmz787_: you can download the logs and do grep
20:35 <@kanzure> nmz787_: do you mean the quantum fireball thing
20:36 < nmz787_> Yeah, found it
20:36 < nmz787_> Sending to roommate
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20:56 < JayDugger> Good evening, everyone.
21:06 <@kanzure> so why haven't we extracted dinosaur dna yet?
21:07 < yashgaroth> not much left to extract
21:07 <@kanzure> yashgaroth: i'm pretty sure we've found old fossilized tissue somewhere?
21:08 < 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
21:09 <@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
21:10 <@kanzure> i'd like to see those estimates
21:11 < yashgaroth> hahaha "The Dinosaur DNA was later revealed to be human Y-Chromosome"
21:12 < 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
21:13 < yashgaroth> you lost me at whatever that is
21:14 <@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?
21:15 < yashgaroth> to the serveratory!
21:16 <@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)
21:17 <@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
21:19 < nmz787__> Kanzure, so whats your ability to move if i move out there?
21:19 < nmz787__> Still have will?
21:20 <@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
21:21 <@kanzure> nmz787__: why should i move? i have comparatively cheap housing
21:22 < 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
21:23 <@kanzure> nyc is super expensive. i guess i'm already paying nyc income tax a few times over, so maybe it makes sense..
21:24 <@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
21:25 < 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"
21:26 <@kanzure> meh proteins
21:26 <@kanzure> why wouldn't dna survive in amber?
21:26 < nmz787__> Nuclease ribozymes
21:27 < yashgaroth> it'd survive better than protein
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21:33 <@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
21:34 <@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)
21:35 <@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
21:39 <@kanzure> like.. why would you use pcr if you haven't identified a single dna molecule yet?
21:40 < yashgaroth> what other methods could you use? except possibly nanopores, which came about after this paper
21:41 <@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
21:42 < 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??
21:43 < yashgaroth> all of them, basically
21:43 <@kanzure> "We have used a range of PCR conditions and primers"
21:44 <@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
21:45 <@kanzure> so it looks like the current upper limit (according to that paper) is 100,000 years
21:46 < yashgaroth> there were some reports about germinating seeds from permafrost that were a few thousands years old
21:46 < yashgaroth> of years*
21:47 <@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
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21:49 < yashgaroth> at that point you can only assume there's DNA, EM detection of it is almost impossible outside of tightly controlled setups
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21:50 <@kanzure> "Non-destructive sampling of ancient insect DNA" neat
21:50 <@kanzure> "A statistical approach to identify ancient template DNA"
21:52 <@kanzure> "Evaluating the Impact of Post-Mortem Damage in Ancient DNA: A Theoretical Approach" but 2011? bleh
21:53 < yashgaroth> I'd say it's at best 50/50 that even a god could assemble a dinosaur genome
21:56 <@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)."
21:57 <@kanzure> *Hofreiter
21:57 <@kanzure> that ref is http://email.eva.mpg.de/~paabo/pdf1/HofreiterAncDNA_NatRev2001.pdf
21:58 <@kanzure> oh god the typesetting
22:01 <@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
22:03 < yashgaroth> 100k years seems like a high estimate, since it would imply frozen DNA would last at lot longer
22:04 <@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
22:06 <@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
22:07 < yashgaroth> the idea of a half-life of DNA is wildly unspecific
22:07 <@kanzure> and hilarious
22:10 < 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
22:11 < yashgaroth> on an unrelated note, another person on biohack has volunteered a grandparent
22:12 <@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
22:14 < yashgaroth> when "I just want to become the galaxy-sized octoflyrhino I've always wanted to be" is considered practically normal
22:15 <@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
22:16 <@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*
22:17 <@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"
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22:19 < 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
22:20 < 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
22:21 < 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
22:22 < yashgaroth> rather than working on quantum computing or anything actually relevant to the next thousand years
22:24 <@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
22:25 < yashgaroth> yes, but that's actually relevant
22:26 < yashgaroth> figuring out the best way to make dolphins able to talk about fish is...less so
22:27 <@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
22:28 < yashgaroth> I'm not suggesting anything outside of STEM is a waste of brainpower, per se
22:29 <@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
22:30 < strangewarp> Rational topology is required, and that's something few people realize
22:31 < 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
22:32 < 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"
22:33 <@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.
22:34 < 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
22:38  * yashgaroth goes to scavenge for food
22:40 < 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
22:41 < skorket> one doesn't need to be sacrificed for the other
22:56 < yashgaroth> one can only hope
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--- Log closed Sat May 12 00:00:08 2012